Starting phenix.real_space_refine on Tue Jan 14 14:46:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f9t_50260/01_2025/9f9t_50260.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f9t_50260/01_2025/9f9t_50260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f9t_50260/01_2025/9f9t_50260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f9t_50260/01_2025/9f9t_50260.map" model { file = "/net/cci-nas-00/data/ceres_data/9f9t_50260/01_2025/9f9t_50260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f9t_50260/01_2025/9f9t_50260.cif" } resolution = 2.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 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 322 5.16 5 C 30544 2.51 5 N 8354 2.21 5 O 10504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 438 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 49724 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1884 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain: "B" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2098 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 10, 'TRANS': 256} Chain: "D" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1864 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 4, 'TRANS': 229} Chain: "E" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1778 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "F" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 8, 'TRANS': 211} Chain breaks: 2 Chain: "G" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1724 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain: "H" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1723 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "I" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1663 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "J" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1555 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "K" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1586 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 201} Chain: "L" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1569 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 1, 'TRANS': 198} Chain: "M" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1654 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain breaks: 1 Chain: "N" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1695 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "F" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "I" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "J" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "K" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "L" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "M" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "N" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "P" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "Q" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "S" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "U" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "V" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "W" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "X" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "Y" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "Z" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "a" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "b" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Restraints were copied for chains: Z, R, P, O, S, b, X, Q, Y, T, a, V, U, W Time building chain proxies: 20.79, per 1000 atoms: 0.42 Number of scatterers: 49724 At special positions: 0 Unit cell: (139.26, 177.54, 137.28, 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 322 16.00 O 10504 8.00 N 8354 7.00 C 30544 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 Time building additional restraints: 8.74 Conformation dependent library (CDL) restraints added in 4.6 seconds 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11536 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 70 sheets defined 38.9% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.96 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 removed outlier: 3.585A pdb=" N VAL A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 80 through 103 Processing helix chain 'A' and resid 107 through 125 removed outlier: 3.743A pdb=" N ARG A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.716A pdb=" N LYS A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 194 through 211 removed outlier: 3.596A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 235 through 249 removed outlier: 3.613A pdb=" N VAL A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 77 through 100 removed outlier: 3.583A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 Processing helix chain 'B' and resid 164 through 176 removed outlier: 3.542A pdb=" N LYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.556A pdb=" N GLU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 231 removed outlier: 3.514A pdb=" N TYR B 227 " --> pdb=" O GLN B 223 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 231 " --> pdb=" O TYR B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 18 through 30 removed outlier: 3.614A pdb=" N ILE C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 108 Processing helix chain 'C' and resid 112 through 130 removed outlier: 3.831A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 185 removed outlier: 3.530A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 207 removed outlier: 3.527A pdb=" N THR C 205 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 262 through 267 removed outlier: 3.638A pdb=" N ALA C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 29 Processing helix chain 'D' and resid 76 through 99 Processing helix chain 'D' and resid 103 through 118 Processing helix chain 'D' and resid 164 through 176 removed outlier: 3.608A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 218 through 231 removed outlier: 3.550A pdb=" N LEU D 222 " --> pdb=" O GLY D 218 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 33 removed outlier: 3.567A pdb=" N LEU E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 3.715A pdb=" N ASN E 65 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 104 removed outlier: 3.758A pdb=" N ILE E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 121 removed outlier: 3.810A pdb=" N LEU E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER E 120 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL E 121 " --> pdb=" O CYS E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 178 Processing helix chain 'E' and resid 180 through 185 Processing helix chain 'E' and resid 190 through 206 removed outlier: 3.867A pdb=" N VAL E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 241 removed outlier: 3.783A pdb=" N ARG E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE E 238 " --> pdb=" O LYS E 234 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 241 " --> pdb=" O ARG E 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 31 removed outlier: 3.879A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 101 Processing helix chain 'F' and resid 105 through 120 removed outlier: 3.556A pdb=" N HIS F 120 " --> pdb=" O LYS F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 177 removed outlier: 4.137A pdb=" N ALA F 169 " --> pdb=" O ARG F 165 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS F 175 " --> pdb=" O THR F 171 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS F 176 " --> pdb=" O TYR F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 180 No H-bonds generated for 'chain 'F' and resid 178 through 180' Processing helix chain 'F' and resid 184 through 198 removed outlier: 3.515A pdb=" N ILE F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.070A pdb=" N LYS F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR F 233 " --> pdb=" O ALA F 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 32 removed outlier: 3.631A pdb=" N VAL G 29 " --> pdb=" O ALA G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 102 Processing helix chain 'G' and resid 106 through 121 removed outlier: 3.953A pdb=" N TYR G 121 " --> pdb=" O PHE G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 175 removed outlier: 3.509A pdb=" N THR G 172 " --> pdb=" O THR G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 198 removed outlier: 3.779A pdb=" N VAL G 189 " --> pdb=" O ASP G 185 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR G 192 " --> pdb=" O VAL G 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 125 Processing helix chain 'H' and resid 129 through 144 removed outlier: 3.532A pdb=" N ALA H 133 " --> pdb=" O ASN H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 188 removed outlier: 3.894A pdb=" N ILE H 187 " --> pdb=" O SER H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 197 Processing helix chain 'H' and resid 202 through 219 Processing helix chain 'H' and resid 244 through 248 Processing helix chain 'H' and resid 255 through 259 Processing helix chain 'I' and resid 114 through 137 Processing helix chain 'I' and resid 141 through 156 removed outlier: 3.603A pdb=" N TYR I 156 " --> pdb=" O HIS I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 208 removed outlier: 3.627A pdb=" N ALA I 203 " --> pdb=" O ALA I 199 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR I 206 " --> pdb=" O SER I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 232 removed outlier: 3.501A pdb=" N GLY I 228 " --> pdb=" O ALA I 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 79 Processing helix chain 'J' and resid 83 through 98 removed outlier: 3.662A pdb=" N ALA J 98 " --> pdb=" O MET J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 154 removed outlier: 3.996A pdb=" N GLY J 148 " --> pdb=" O GLU J 144 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 176 Processing helix chain 'K' and resid 50 through 71 Processing helix chain 'K' and resid 78 through 95 removed outlier: 3.662A pdb=" N ARG K 95 " --> pdb=" O ALA K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 158 Processing helix chain 'K' and resid 163 through 182 Processing helix chain 'L' and resid 158 through 180 removed outlier: 3.587A pdb=" N GLU L 177 " --> pdb=" O CYS L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 200 Processing helix chain 'L' and resid 201 through 204 removed outlier: 4.329A pdb=" N GLY L 204 " --> pdb=" O ARG L 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 201 through 204' Processing helix chain 'L' and resid 241 through 253 removed outlier: 4.804A pdb=" N GLY L 247 " --> pdb=" O ILE L 243 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL L 248 " --> pdb=" O TYR L 244 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN L 251 " --> pdb=" O GLY L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 277 removed outlier: 3.585A pdb=" N ARG L 276 " --> pdb=" O HIS L 272 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 309 removed outlier: 3.624A pdb=" N ASP L 307 " --> pdb=" O THR L 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 110 Processing helix chain 'M' and resid 117 through 131 Processing helix chain 'M' and resid 174 through 188 Proline residue: M 180 - end of helix Processing helix chain 'M' and resid 200 through 219 Processing helix chain 'N' and resid 53 through 73 Processing helix chain 'N' and resid 79 through 97 Processing helix chain 'N' and resid 136 through 141 Processing helix chain 'N' and resid 141 through 149 Processing helix chain 'N' and resid 156 through 175 Processing helix chain 'N' and resid 206 through 209 Processing helix chain 'N' and resid 210 through 215 Processing helix chain 'O' and resid 19 through 32 removed outlier: 3.585A pdb=" N VAL O 29 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR O 30 " --> pdb=" O PHE O 26 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 63 Processing helix chain 'O' and resid 80 through 103 Processing helix chain 'O' and resid 107 through 125 removed outlier: 3.745A pdb=" N ARG O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 186 removed outlier: 3.716A pdb=" N LYS O 186 " --> pdb=" O GLU O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 193 Processing helix chain 'O' and resid 194 through 211 removed outlier: 3.597A pdb=" N ILE O 201 " --> pdb=" O ASP O 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 215 through 217 No H-bonds generated for 'chain 'O' and resid 215 through 217' Processing helix chain 'O' and resid 235 through 249 removed outlier: 3.612A pdb=" N VAL O 239 " --> pdb=" O PRO O 235 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP O 242 " --> pdb=" O ASP O 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 27 Processing helix chain 'P' and resid 77 through 100 removed outlier: 3.583A pdb=" N VAL P 83 " --> pdb=" O PRO P 79 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU P 84 " --> pdb=" O ASP P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 119 Processing helix chain 'P' and resid 164 through 176 removed outlier: 3.545A pdb=" N LYS P 174 " --> pdb=" O THR P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 197 removed outlier: 3.555A pdb=" N GLU P 195 " --> pdb=" O LEU P 191 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY P 196 " --> pdb=" O THR P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 231 removed outlier: 3.518A pdb=" N TYR P 227 " --> pdb=" O GLN P 223 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN P 230 " --> pdb=" O ASP P 226 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE P 231 " --> pdb=" O TYR P 227 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 6 Processing helix chain 'Q' and resid 18 through 30 removed outlier: 3.612A pdb=" N ILE Q 28 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 108 Processing helix chain 'Q' and resid 112 through 130 removed outlier: 3.831A pdb=" N TYR Q 127 " --> pdb=" O GLU Q 123 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR Q 128 " --> pdb=" O LYS Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 185 removed outlier: 3.532A pdb=" N LEU Q 180 " --> pdb=" O VAL Q 176 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 207 removed outlier: 3.528A pdb=" N THR Q 205 " --> pdb=" O VAL Q 201 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP Q 207 " --> pdb=" O GLY Q 203 " (cutoff:3.500A) Processing helix chain 'Q' and resid 254 through 259 Processing helix chain 'Q' and resid 262 through 267 removed outlier: 3.637A pdb=" N ALA Q 267 " --> pdb=" O ARG Q 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 29 Processing helix chain 'R' and resid 76 through 99 Processing helix chain 'R' and resid 103 through 118 Processing helix chain 'R' and resid 164 through 176 removed outlier: 3.606A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 194 Processing helix chain 'R' and resid 218 through 231 removed outlier: 3.545A pdb=" N LEU R 222 " --> pdb=" O GLY R 218 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE R 225 " --> pdb=" O GLU R 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 33 removed outlier: 3.566A pdb=" N LEU S 33 " --> pdb=" O GLU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 65 removed outlier: 3.711A pdb=" N ASN S 65 " --> pdb=" O SER S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 104 removed outlier: 3.757A pdb=" N ILE S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 121 removed outlier: 3.809A pdb=" N LEU S 119 " --> pdb=" O ALA S 115 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER S 120 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL S 121 " --> pdb=" O CYS S 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 173 through 178 Processing helix chain 'S' and resid 180 through 185 Processing helix chain 'S' and resid 190 through 206 removed outlier: 3.865A pdb=" N VAL S 199 " --> pdb=" O GLU S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 232 through 241 removed outlier: 3.784A pdb=" N ARG S 237 " --> pdb=" O THR S 233 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE S 238 " --> pdb=" O LYS S 234 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG S 241 " --> pdb=" O ARG S 237 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 31 removed outlier: 3.879A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 101 Processing helix chain 'T' and resid 105 through 120 removed outlier: 3.555A pdb=" N HIS T 120 " --> pdb=" O LYS T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 165 through 177 removed outlier: 4.137A pdb=" N ALA T 169 " --> pdb=" O ARG T 165 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS T 175 " --> pdb=" O THR T 171 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS T 176 " --> pdb=" O TYR T 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 178 through 180 No H-bonds generated for 'chain 'T' and resid 178 through 180' Processing helix chain 'T' and resid 184 through 198 removed outlier: 3.517A pdb=" N ILE T 189 " --> pdb=" O LEU T 185 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 234 removed outlier: 4.074A pdb=" N LYS T 232 " --> pdb=" O GLU T 228 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR T 233 " --> pdb=" O ALA T 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 32 removed outlier: 3.632A pdb=" N VAL U 29 " --> pdb=" O ALA U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 102 Processing helix chain 'U' and resid 106 through 121 removed outlier: 3.951A pdb=" N TYR U 121 " --> pdb=" O PHE U 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 166 through 175 removed outlier: 3.508A pdb=" N THR U 172 " --> pdb=" O THR U 168 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 198 removed outlier: 3.778A pdb=" N VAL U 189 " --> pdb=" O ASP U 185 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR U 192 " --> pdb=" O VAL U 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 102 through 125 Processing helix chain 'V' and resid 129 through 144 removed outlier: 3.532A pdb=" N ALA V 133 " --> pdb=" O ASN V 129 " (cutoff:3.500A) Processing helix chain 'V' and resid 183 through 188 removed outlier: 3.891A pdb=" N ILE V 187 " --> pdb=" O SER V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 189 through 197 Processing helix chain 'V' and resid 202 through 219 Processing helix chain 'V' and resid 244 through 248 Processing helix chain 'V' and resid 255 through 259 Processing helix chain 'W' and resid 114 through 137 Processing helix chain 'W' and resid 141 through 156 removed outlier: 3.605A pdb=" N TYR W 156 " --> pdb=" O HIS W 152 " (cutoff:3.500A) Processing helix chain 'W' and resid 196 through 208 removed outlier: 3.627A pdb=" N ALA W 203 " --> pdb=" O ALA W 199 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR W 206 " --> pdb=" O SER W 202 " (cutoff:3.500A) Processing helix chain 'W' and resid 213 through 232 removed outlier: 3.501A pdb=" N GLY W 228 " --> pdb=" O ALA W 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 79 Processing helix chain 'X' and resid 83 through 98 removed outlier: 3.662A pdb=" N ALA X 98 " --> pdb=" O MET X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 154 removed outlier: 3.995A pdb=" N GLY X 148 " --> pdb=" O GLU X 144 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET X 149 " --> pdb=" O SER X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 159 through 176 Processing helix chain 'Y' and resid 50 through 71 Processing helix chain 'Y' and resid 78 through 95 removed outlier: 3.663A pdb=" N ARG Y 95 " --> pdb=" O ALA Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 146 through 158 Processing helix chain 'Y' and resid 163 through 182 Processing helix chain 'Z' and resid 158 through 181 removed outlier: 3.585A pdb=" N GLU Z 177 " --> pdb=" O CYS Z 173 " (cutoff:3.500A) Processing helix chain 'Z' and resid 185 through 200 Processing helix chain 'Z' and resid 201 through 204 removed outlier: 4.329A pdb=" N GLY Z 204 " --> pdb=" O ARG Z 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 201 through 204' Processing helix chain 'Z' and resid 241 through 253 removed outlier: 4.804A pdb=" N GLY Z 247 " --> pdb=" O ILE Z 243 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL Z 248 " --> pdb=" O TYR Z 244 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN Z 251 " --> pdb=" O GLY Z 247 " (cutoff:3.500A) Processing helix chain 'Z' and resid 258 through 277 removed outlier: 3.585A pdb=" N ARG Z 276 " --> pdb=" O HIS Z 272 " (cutoff:3.500A) Processing helix chain 'Z' and resid 302 through 309 removed outlier: 3.623A pdb=" N ASP Z 307 " --> pdb=" O THR Z 303 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 110 Processing helix chain 'a' and resid 117 through 131 Processing helix chain 'a' and resid 174 through 188 Proline residue: a 180 - end of helix Processing helix chain 'a' and resid 200 through 219 Processing helix chain 'b' and resid 53 through 73 Processing helix chain 'b' and resid 79 through 97 Processing helix chain 'b' and resid 136 through 141 Processing helix chain 'b' and resid 141 through 149 Processing helix chain 'b' and resid 156 through 175 Processing helix chain 'b' and resid 206 through 209 Processing helix chain 'b' and resid 210 through 215 Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171 removed outlier: 6.467A pdb=" N LEU A 35 " --> pdb=" O GLN A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 161 Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 67 removed outlier: 6.622A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 167 through 170 Processing sheet with id=AA6, first strand: chain 'C' and resid 71 through 75 removed outlier: 6.490A pdb=" N ILE C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP C 146 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU C 153 " --> pdb=" O TRP C 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.594A pdb=" N LYS D 213 " --> pdb=" O GLU D 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 62 through 66 removed outlier: 6.564A pdb=" N ILE D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.540A pdb=" N ILE E 67 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU E 78 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU E 69 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP E 147 " --> pdb=" O GLY E 150 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY E 150 " --> pdb=" O ASP E 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 159 through 162 removed outlier: 7.182A pdb=" N ILE F 213 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL F 224 " --> pdb=" O ILE F 213 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE F 215 " --> pdb=" O PHE F 222 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE F 222 " --> pdb=" O ILE F 215 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 64 through 68 removed outlier: 6.467A pdb=" N VAL F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 160 through 163 Processing sheet with id=AB5, first strand: chain 'G' and resid 65 through 69 removed outlier: 6.424A pdb=" N ALA G 72 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA G 140 " --> pdb=" O GLY G 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 179 through 182 Processing sheet with id=AB7, first strand: chain 'H' and resid 74 through 75 Processing sheet with id=AB8, first strand: chain 'H' and resid 88 through 92 removed outlier: 6.367A pdb=" N ILE H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL H 165 " --> pdb=" O LEU H 177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 190 through 193 removed outlier: 6.682A pdb=" N VAL I 239 " --> pdb=" O GLY I 254 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY I 254 " --> pdb=" O VAL I 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 86 through 88 removed outlier: 6.184A pdb=" N GLU I 88 " --> pdb=" O VAL I 92 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 100 through 104 removed outlier: 6.782A pdb=" N ILE I 100 " --> pdb=" O GLY I 111 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY I 111 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR I 102 " --> pdb=" O CYS I 109 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N CYS I 109 " --> pdb=" O TYR I 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 277 through 281 removed outlier: 3.556A pdb=" N ARG I 279 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N SER J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.814A pdb=" N LEU J 28 " --> pdb=" O ILE J 35 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 42 through 44 Processing sheet with id=AC6, first strand: chain 'K' and resid 140 through 143 removed outlier: 4.557A pdb=" N CYS K 191 " --> pdb=" O VAL K 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 22 through 24 removed outlier: 6.375A pdb=" N PHE K 24 " --> pdb=" O LYS K 28 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LYS K 28 " --> pdb=" O PHE K 24 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 36 through 40 removed outlier: 6.469A pdb=" N LYS K 43 " --> pdb=" O LEU K 39 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU K 126 " --> pdb=" O VAL K 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 235 through 238 removed outlier: 6.268A pdb=" N VAL L 284 " --> pdb=" O ARG L 299 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG L 299 " --> pdb=" O VAL L 284 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL L 286 " --> pdb=" O ILE L 297 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 130 through 131 removed outlier: 3.591A pdb=" N SER L 138 " --> pdb=" O ALA L 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 144 through 146 removed outlier: 3.966A pdb=" N MET L 210 " --> pdb=" O THR L 154 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 168 through 172 removed outlier: 5.459A pdb=" N THR M 42 " --> pdb=" O ASP M 57 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 60 through 62 removed outlier: 5.938A pdb=" N GLY M 62 " --> pdb=" O ILE M 66 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ILE M 66 " --> pdb=" O GLY M 62 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 75 through 79 removed outlier: 6.432A pdb=" N THR M 82 " --> pdb=" O LEU M 78 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN M 141 " --> pdb=" O TYR M 157 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER M 156 " --> pdb=" O GLU M 164 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU M 164 " --> pdb=" O SER M 156 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.731A pdb=" N LEU N 24 " --> pdb=" O LYS N 31 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR N 45 " --> pdb=" O VAL N 41 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.731A pdb=" N LEU N 24 " --> pdb=" O LYS N 31 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 131 through 134 Processing sheet with id=AD9, first strand: chain 'O' and resid 167 through 171 removed outlier: 6.471A pdb=" N LEU O 35 " --> pdb=" O GLN O 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 66 through 68 Processing sheet with id=AE2, first strand: chain 'P' and resid 158 through 161 Processing sheet with id=AE3, first strand: chain 'P' and resid 64 through 67 removed outlier: 6.620A pdb=" N VAL P 70 " --> pdb=" O LEU P 66 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 167 through 170 Processing sheet with id=AE5, first strand: chain 'Q' and resid 71 through 75 removed outlier: 6.491A pdb=" N ILE Q 78 " --> pdb=" O ILE Q 74 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP Q 146 " --> pdb=" O GLY Q 150 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU Q 153 " --> pdb=" O TRP Q 165 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 158 through 161 removed outlier: 3.592A pdb=" N LYS R 213 " --> pdb=" O GLU R 210 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 62 through 66 removed outlier: 6.564A pdb=" N ILE R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 167 through 170 Processing sheet with id=AE9, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.539A pdb=" N ILE S 67 " --> pdb=" O LEU S 78 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU S 78 " --> pdb=" O ILE S 67 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU S 69 " --> pdb=" O THR S 76 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR S 76 " --> pdb=" O GLU S 69 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP S 147 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY S 150 " --> pdb=" O ASP S 147 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 159 through 162 removed outlier: 7.180A pdb=" N ILE T 213 " --> pdb=" O VAL T 224 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL T 224 " --> pdb=" O ILE T 213 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE T 215 " --> pdb=" O PHE T 222 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE T 222 " --> pdb=" O ILE T 215 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 64 through 68 removed outlier: 6.469A pdb=" N VAL T 71 " --> pdb=" O LEU T 67 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 160 through 163 Processing sheet with id=AF4, first strand: chain 'U' and resid 65 through 69 removed outlier: 6.424A pdb=" N ALA U 72 " --> pdb=" O VAL U 68 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA U 140 " --> pdb=" O GLY U 143 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 179 through 182 Processing sheet with id=AF6, first strand: chain 'V' and resid 74 through 75 Processing sheet with id=AF7, first strand: chain 'V' and resid 88 through 92 removed outlier: 6.367A pdb=" N ILE V 95 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL V 165 " --> pdb=" O LEU V 177 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 190 through 193 removed outlier: 6.680A pdb=" N VAL W 239 " --> pdb=" O GLY W 254 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY W 254 " --> pdb=" O VAL W 239 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 86 through 88 removed outlier: 6.185A pdb=" N GLU W 88 " --> pdb=" O VAL W 92 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL W 92 " --> pdb=" O GLU W 88 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 100 through 104 removed outlier: 6.782A pdb=" N ILE W 100 " --> pdb=" O GLY W 111 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLY W 111 " --> pdb=" O ILE W 100 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TYR W 102 " --> pdb=" O CYS W 109 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N CYS W 109 " --> pdb=" O TYR W 102 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 277 through 281 removed outlier: 3.558A pdb=" N ARG W 279 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N SER X 10 " --> pdb=" O ASP X 25 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 28 through 30 removed outlier: 6.814A pdb=" N LEU X 28 " --> pdb=" O ILE X 35 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 42 through 44 Processing sheet with id=AG5, first strand: chain 'Y' and resid 140 through 143 removed outlier: 4.565A pdb=" N CYS Y 191 " --> pdb=" O VAL Y 202 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 22 through 24 removed outlier: 6.374A pdb=" N PHE Y 24 " --> pdb=" O LYS Y 28 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LYS Y 28 " --> pdb=" O PHE Y 24 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 36 through 40 removed outlier: 6.469A pdb=" N LYS Y 43 " --> pdb=" O LEU Y 39 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU Y 126 " --> pdb=" O VAL Y 138 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 235 through 238 removed outlier: 6.266A pdb=" N VAL Z 284 " --> pdb=" O ARG Z 299 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG Z 299 " --> pdb=" O VAL Z 284 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL Z 286 " --> pdb=" O ILE Z 297 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 130 through 131 removed outlier: 3.589A pdb=" N SER Z 138 " --> pdb=" O ALA Z 130 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 144 through 146 removed outlier: 3.965A pdb=" N MET Z 210 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'a' and resid 168 through 172 removed outlier: 5.457A pdb=" N THR a 42 " --> pdb=" O ASP a 57 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 60 through 62 removed outlier: 5.937A pdb=" N GLY a 62 " --> pdb=" O ILE a 66 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE a 66 " --> pdb=" O GLY a 62 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'a' and resid 75 through 79 removed outlier: 6.433A pdb=" N THR a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN a 141 " --> pdb=" O TYR a 157 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER a 156 " --> pdb=" O GLU a 164 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU a 164 " --> pdb=" O SER a 156 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 29 through 32 removed outlier: 6.732A pdb=" N LEU b 24 " --> pdb=" O LYS b 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR b 45 " --> pdb=" O VAL b 41 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 29 through 32 removed outlier: 6.732A pdb=" N LEU b 24 " --> pdb=" O LYS b 31 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 131 through 134 2729 hydrogen bonds defined for protein. 7791 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: 17.29 Time building geometry restraints manager: 10.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 8800 1.31 - 1.46: 17334 1.46 - 1.60: 22776 1.60 - 1.75: 2 1.75 - 1.90: 488 Bond restraints: 49400 Sorted by residual: bond pdb=" CA SER H 167 " pdb=" CB SER H 167 " ideal model delta sigma weight residual 1.529 1.429 0.100 1.43e-02 4.89e+03 4.93e+01 bond pdb=" CA SER V 167 " pdb=" CB SER V 167 " ideal model delta sigma weight residual 1.529 1.429 0.100 1.43e-02 4.89e+03 4.89e+01 bond pdb=" C PRO b 36 " pdb=" O PRO b 36 " ideal model delta sigma weight residual 1.235 1.184 0.051 7.90e-03 1.60e+04 4.25e+01 bond pdb=" C PRO N 36 " pdb=" O PRO N 36 " ideal model delta sigma weight residual 1.235 1.184 0.051 7.90e-03 1.60e+04 4.25e+01 bond pdb=" CA SER V 72 " pdb=" CB SER V 72 " ideal model delta sigma weight residual 1.528 1.440 0.089 1.39e-02 5.18e+03 4.07e+01 ... (remaining 49395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.59: 64534 4.59 - 9.18: 2222 9.18 - 13.77: 78 13.77 - 18.37: 6 18.37 - 22.96: 2 Bond angle restraints: 66842 Sorted by residual: angle pdb=" C PHE a 177 " pdb=" CA PHE a 177 " pdb=" CB PHE a 177 " ideal model delta sigma weight residual 109.03 86.07 22.96 1.62e+00 3.81e-01 2.01e+02 angle pdb=" C PHE M 177 " pdb=" CA PHE M 177 " pdb=" CB PHE M 177 " ideal model delta sigma weight residual 109.03 86.09 22.94 1.62e+00 3.81e-01 2.00e+02 angle pdb=" N TYR X 136 " pdb=" CA TYR X 136 " pdb=" CB TYR X 136 " ideal model delta sigma weight residual 111.46 96.60 14.86 1.54e+00 4.22e-01 9.31e+01 angle pdb=" N TYR J 136 " pdb=" CA TYR J 136 " pdb=" CB TYR J 136 " ideal model delta sigma weight residual 111.46 96.63 14.83 1.54e+00 4.22e-01 9.27e+01 angle pdb=" CA THR a 127 " pdb=" CB THR a 127 " pdb=" OG1 THR a 127 " ideal model delta sigma weight residual 109.60 95.69 13.91 1.50e+00 4.44e-01 8.60e+01 ... (remaining 66837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 25997 17.94 - 35.88: 2636 35.88 - 53.82: 668 53.82 - 71.76: 217 71.76 - 89.71: 78 Dihedral angle restraints: 29596 sinusoidal: 11546 harmonic: 18050 Sorted by residual: dihedral pdb=" C PHE M 177 " pdb=" N PHE M 177 " pdb=" CA PHE M 177 " pdb=" CB PHE M 177 " ideal model delta harmonic sigma weight residual -122.60 -101.36 -21.24 0 2.50e+00 1.60e-01 7.22e+01 dihedral pdb=" C PHE a 177 " pdb=" N PHE a 177 " pdb=" CA PHE a 177 " pdb=" CB PHE a 177 " ideal model delta harmonic sigma weight residual -122.60 -101.38 -21.22 0 2.50e+00 1.60e-01 7.20e+01 dihedral pdb=" C CYS b 103 " pdb=" N CYS b 103 " pdb=" CA CYS b 103 " pdb=" CB CYS b 103 " ideal model delta harmonic sigma weight residual -122.60 -104.28 -18.32 0 2.50e+00 1.60e-01 5.37e+01 ... (remaining 29593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4659 0.089 - 0.178: 2188 0.178 - 0.267: 556 0.267 - 0.356: 87 0.356 - 0.445: 16 Chirality restraints: 7506 Sorted by residual: chirality pdb=" CA TYR V 218 " pdb=" N TYR V 218 " pdb=" C TYR V 218 " pdb=" CB TYR V 218 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CA TYR H 218 " pdb=" N TYR H 218 " pdb=" C TYR H 218 " pdb=" CB TYR H 218 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CA HIS I 143 " pdb=" N HIS I 143 " pdb=" C HIS I 143 " pdb=" CB HIS I 143 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.62e+00 ... (remaining 7503 not shown) Planarity restraints: 8636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 192 " -0.089 2.00e-02 2.50e+03 5.56e-02 5.41e+01 pdb=" CG PHE H 192 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 PHE H 192 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE H 192 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE H 192 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE H 192 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE H 192 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE V 192 " 0.089 2.00e-02 2.50e+03 5.55e-02 5.40e+01 pdb=" CG PHE V 192 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 PHE V 192 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 PHE V 192 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE V 192 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE V 192 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE V 192 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP T 13 " -0.082 2.00e-02 2.50e+03 4.62e-02 5.34e+01 pdb=" CG TRP T 13 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP T 13 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP T 13 " 0.062 2.00e-02 2.50e+03 pdb=" NE1 TRP T 13 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP T 13 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP T 13 " 0.055 2.00e-02 2.50e+03 pdb=" CZ2 TRP T 13 " -0.021 2.00e-02 2.50e+03 pdb=" CZ3 TRP T 13 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP T 13 " -0.055 2.00e-02 2.50e+03 ... (remaining 8633 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 3143 2.69 - 3.24: 46452 3.24 - 3.79: 80459 3.79 - 4.35: 114521 4.35 - 4.90: 183012 Nonbonded interactions: 427587 Sorted by model distance: nonbonded pdb=" OD1 ASP H 194 " pdb=" OH TYR V 258 " model vdw 2.135 3.040 nonbonded pdb=" OH TYR H 258 " pdb=" OD1 ASP V 194 " model vdw 2.135 3.040 nonbonded pdb=" OH TYR M 168 " pdb=" OD1 ASP M 183 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR a 168 " pdb=" OD1 ASP a 183 " model vdw 2.179 3.040 nonbonded pdb=" OH TYR H 218 " pdb=" O HOH H 301 " model vdw 2.207 3.040 ... (remaining 427582 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: 0.18 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'b' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'W' } 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 individual isotropic 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: 4.360 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: 0.060 Extract box with map and model: 1.510 Check model and map are aligned: 0.290 Set scattering table: 0.350 Process input model: 82.080 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.260 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: 0.010 Load rotamer database and sin/cos tables:8.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 : 0.014 0.119 49400 Z= 0.936 Angle : 2.025 22.958 66842 Z= 1.334 Chirality : 0.104 0.445 7506 Planarity : 0.020 0.245 8636 Dihedral : 16.996 89.706 18060 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.96 % Favored : 95.50 % Rotamer: Outliers : 5.78 % Allowed : 8.82 % Favored : 85.40 % Cbeta Deviations : 1.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.09), residues: 6194 helix: -2.56 (0.08), residues: 2282 sheet: -0.25 (0.13), residues: 1416 loop : -1.70 (0.11), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.017 TRP T 13 HIS 0.049 0.008 HIS F 100 PHE 0.089 0.016 PHE H 192 TYR 0.086 0.016 TYR T 117 ARG 0.047 0.005 ARG b 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1377 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 299 poor density : 1078 time to evaluate : 4.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7908 (mttp) cc_final: 0.7693 (mptt) REVERT: A 59 ARG cc_start: 0.8475 (ttt90) cc_final: 0.8192 (mmm-85) REVERT: A 94 GLU cc_start: 0.8552 (tp30) cc_final: 0.8317 (tp30) REVERT: A 173 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7937 (ttmm) REVERT: A 178 ASN cc_start: 0.8240 (m-40) cc_final: 0.8010 (m-40) REVERT: A 196 LYS cc_start: 0.8384 (tttt) cc_final: 0.8025 (ttmt) REVERT: A 197 ASP cc_start: 0.8130 (m-30) cc_final: 0.7877 (m-30) REVERT: A 210 LEU cc_start: 0.7392 (mt) cc_final: 0.7021 (mm) REVERT: B 173 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6223 (mm-30) REVERT: B 175 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6380 (mmm160) REVERT: B 179 GLU cc_start: 0.6690 (mp0) cc_final: 0.6479 (pm20) REVERT: B 225 LYS cc_start: 0.7193 (ttmt) cc_final: 0.6869 (tptt) REVERT: B 227 TYR cc_start: 0.7505 (m-80) cc_final: 0.7167 (m-80) REVERT: C 8 ARG cc_start: 0.6870 (mtt-85) cc_final: 0.6485 (mtp85) REVERT: C 30 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7202 (mp10) REVERT: C 69 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6451 (tt0) REVERT: C 118 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7929 (mtm110) REVERT: C 166 ARG cc_start: 0.8330 (mtt180) cc_final: 0.8050 (mtp180) REVERT: C 172 GLN cc_start: 0.6611 (mt0) cc_final: 0.6304 (mt0) REVERT: C 184 ASP cc_start: 0.7112 (m-30) cc_final: 0.6350 (t0) REVERT: C 192 ASP cc_start: 0.7026 (m-30) cc_final: 0.6666 (m-30) REVERT: C 202 LEU cc_start: 0.7293 (mt) cc_final: 0.7009 (mt) REVERT: C 214 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6495 (mm-30) REVERT: C 215 ARG cc_start: 0.7417 (mtp180) cc_final: 0.6941 (mtp85) REVERT: C 231 LYS cc_start: 0.6940 (mttt) cc_final: 0.6711 (mttm) REVERT: C 241 LYS cc_start: 0.7188 (mttt) cc_final: 0.6780 (tptp) REVERT: D 15 HIS cc_start: 0.6561 (m170) cc_final: 0.6306 (m90) REVERT: D 30 LEU cc_start: 0.7051 (mt) cc_final: 0.6835 (mt) REVERT: D 55 ASP cc_start: 0.7407 (t70) cc_final: 0.7010 (t70) REVERT: D 105 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: D 143 HIS cc_start: 0.8315 (m170) cc_final: 0.7961 (m170) REVERT: D 166 LYS cc_start: 0.7368 (tttt) cc_final: 0.7002 (pmtt) REVERT: D 171 PHE cc_start: 0.7758 (t80) cc_final: 0.7457 (t80) REVERT: D 205 GLU cc_start: 0.7540 (pt0) cc_final: 0.7335 (pt0) REVERT: D 212 LYS cc_start: 0.5882 (tptt) cc_final: 0.5615 (mttp) REVERT: D 217 MET cc_start: 0.5914 (ttp) cc_final: 0.5616 (ttp) REVERT: E 20 ARG cc_start: 0.7688 (mtt90) cc_final: 0.7372 (mtt90) REVERT: E 25 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7350 (mm-30) REVERT: E 60 ASP cc_start: 0.7012 (m-30) cc_final: 0.6791 (m-30) REVERT: E 62 SER cc_start: 0.7009 (OUTLIER) cc_final: 0.6259 (t) REVERT: E 64 MET cc_start: 0.7075 (mtp) cc_final: 0.6870 (mmm) REVERT: E 122 ARG cc_start: 0.6938 (mtt90) cc_final: 0.6628 (ttm-80) REVERT: E 133 MET cc_start: 0.7398 (mtm) cc_final: 0.7156 (mtp) REVERT: E 166 ASP cc_start: 0.7611 (m-30) cc_final: 0.7284 (m-30) REVERT: E 184 ILE cc_start: 0.6088 (mt) cc_final: 0.5836 (mp) REVERT: E 187 ARG cc_start: 0.5284 (mmm-85) cc_final: 0.5065 (tpp80) REVERT: E 195 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6954 (mt-10) REVERT: E 200 ARG cc_start: 0.6335 (ttm-80) cc_final: 0.6052 (ttt-90) REVERT: E 206 MET cc_start: 0.5394 (mtt) cc_final: 0.4987 (tpp) REVERT: E 216 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6514 (tp30) REVERT: F 26 ASN cc_start: 0.8112 (t0) cc_final: 0.7882 (t0) REVERT: F 41 LYS cc_start: 0.8259 (mmtt) cc_final: 0.8042 (tppt) REVERT: F 111 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: F 175 LYS cc_start: 0.8005 (mttt) cc_final: 0.7777 (mtmt) REVERT: G 6 HIS cc_start: 0.7292 (p-80) cc_final: 0.7067 (p-80) REVERT: G 27 LYS cc_start: 0.8303 (tppt) cc_final: 0.8102 (mmtp) REVERT: G 55 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7593 (ptt-90) REVERT: G 58 GLU cc_start: 0.7736 (tp30) cc_final: 0.7529 (mm-30) REVERT: G 116 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8177 (tp30) REVERT: G 173 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7362 (mp0) REVERT: G 193 LYS cc_start: 0.7925 (tttt) cc_final: 0.7684 (ttmm) REVERT: G 204 ASP cc_start: 0.6331 (m-30) cc_final: 0.6042 (m-30) REVERT: G 217 LYS cc_start: 0.7400 (mttp) cc_final: 0.7155 (mmtm) REVERT: H 259 ARG cc_start: 0.7800 (ttp80) cc_final: 0.7313 (ttm110) REVERT: H 280 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7730 (mtp85) REVERT: I 98 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7991 (mmpt) REVERT: I 215 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8316 (tp30) REVERT: I 260 GLU cc_start: 0.5257 (OUTLIER) cc_final: 0.4843 (mm-30) REVERT: I 274 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7480 (m) REVERT: I 281 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7718 (mm-30) REVERT: J 81 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8642 (mm-30) REVERT: J 115 ARG cc_start: 0.5714 (mtt180) cc_final: 0.5384 (mtm180) REVERT: J 132 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: J 149 MET cc_start: 0.7666 (mmm) cc_final: 0.7423 (mmm) REVERT: K 50 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7999 (mp0) REVERT: K 75 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.6289 (mpt90) REVERT: K 78 ARG cc_start: 0.8529 (mtp85) cc_final: 0.8233 (mtt-85) REVERT: K 116 SER cc_start: 0.6004 (OUTLIER) cc_final: 0.5710 (m) REVERT: K 200 GLU cc_start: 0.7944 (pt0) cc_final: 0.7530 (pt0) REVERT: L 117 HIS cc_start: 0.8676 (t-170) cc_final: 0.8473 (t-90) REVERT: L 134 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7726 (tm130) REVERT: L 177 GLU cc_start: 0.8531 (tt0) cc_final: 0.8298 (tt0) REVERT: L 234 GLU cc_start: 0.8350 (pt0) cc_final: 0.8129 (mm-30) REVERT: M 105 GLN cc_start: 0.8623 (tt0) cc_final: 0.8282 (tp-100) REVERT: M 133 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7686 (tpt90) REVERT: M 242 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7811 (pm20) REVERT: N 1 MET cc_start: 0.6028 (mtm) cc_final: 0.5424 (tpt) REVERT: N 26 TYR cc_start: 0.8633 (t80) cc_final: 0.8386 (t80) REVERT: N 99 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8218 (tp30) REVERT: N 114 GLU cc_start: 0.7825 (tt0) cc_final: 0.7581 (tp30) REVERT: N 201 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8128 (mp0) REVERT: N 212 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: O 8 LYS cc_start: 0.7905 (mttp) cc_final: 0.7690 (mptt) REVERT: O 59 ARG cc_start: 0.8478 (ttt90) cc_final: 0.8189 (mmm-85) REVERT: O 94 GLU cc_start: 0.8549 (tp30) cc_final: 0.8317 (tp30) REVERT: O 173 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7934 (ttmm) REVERT: O 178 ASN cc_start: 0.8240 (m-40) cc_final: 0.8003 (m-40) REVERT: O 196 LYS cc_start: 0.8387 (tttt) cc_final: 0.8026 (ttmt) REVERT: O 197 ASP cc_start: 0.8132 (m-30) cc_final: 0.7877 (m-30) REVERT: O 210 LEU cc_start: 0.7388 (mt) cc_final: 0.7018 (mm) REVERT: P 173 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6232 (mm-30) REVERT: P 175 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6372 (mmm160) REVERT: P 179 GLU cc_start: 0.6695 (mp0) cc_final: 0.6481 (pm20) REVERT: P 225 LYS cc_start: 0.7199 (ttmt) cc_final: 0.6874 (tptt) REVERT: P 227 TYR cc_start: 0.7510 (m-80) cc_final: 0.7175 (m-80) REVERT: Q 8 ARG cc_start: 0.6873 (mtt-85) cc_final: 0.6487 (mtp85) REVERT: Q 30 GLN cc_start: 0.7494 (mm-40) cc_final: 0.7201 (mp10) REVERT: Q 69 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6448 (tt0) REVERT: Q 118 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7932 (mtm110) REVERT: Q 166 ARG cc_start: 0.8326 (mtt180) cc_final: 0.8045 (mtp180) REVERT: Q 172 GLN cc_start: 0.6619 (mt0) cc_final: 0.6306 (mt0) REVERT: Q 184 ASP cc_start: 0.7120 (m-30) cc_final: 0.6358 (t0) REVERT: Q 192 ASP cc_start: 0.7020 (m-30) cc_final: 0.6652 (m-30) REVERT: Q 202 LEU cc_start: 0.7293 (mt) cc_final: 0.7009 (mt) REVERT: Q 214 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6510 (mm-30) REVERT: Q 215 ARG cc_start: 0.7428 (mtp180) cc_final: 0.6942 (mtp85) REVERT: Q 231 LYS cc_start: 0.6946 (mttt) cc_final: 0.6715 (mttm) REVERT: Q 241 LYS cc_start: 0.7198 (mttt) cc_final: 0.6780 (tptp) REVERT: R 15 HIS cc_start: 0.6529 (m170) cc_final: 0.6275 (m90) REVERT: R 30 LEU cc_start: 0.7053 (mt) cc_final: 0.6837 (mt) REVERT: R 55 ASP cc_start: 0.7409 (t70) cc_final: 0.7013 (t70) REVERT: R 105 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: R 143 HIS cc_start: 0.8315 (m170) cc_final: 0.7960 (m170) REVERT: R 166 LYS cc_start: 0.7375 (tttt) cc_final: 0.7015 (pmtt) REVERT: R 205 GLU cc_start: 0.7544 (pt0) cc_final: 0.7339 (pt0) REVERT: R 212 LYS cc_start: 0.5871 (tptt) cc_final: 0.5614 (mttp) REVERT: R 217 MET cc_start: 0.5902 (ttp) cc_final: 0.5605 (ttp) REVERT: S 20 ARG cc_start: 0.7694 (mtt90) cc_final: 0.7376 (mtt90) REVERT: S 25 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7346 (mm-30) REVERT: S 60 ASP cc_start: 0.7017 (m-30) cc_final: 0.6780 (m-30) REVERT: S 62 SER cc_start: 0.7019 (OUTLIER) cc_final: 0.6269 (t) REVERT: S 122 ARG cc_start: 0.6944 (mtt90) cc_final: 0.6629 (ttm-80) REVERT: S 133 MET cc_start: 0.7403 (mtm) cc_final: 0.7140 (mtp) REVERT: S 166 ASP cc_start: 0.7612 (m-30) cc_final: 0.7287 (m-30) REVERT: S 184 ILE cc_start: 0.6093 (mt) cc_final: 0.5841 (mp) REVERT: S 187 ARG cc_start: 0.5284 (mmm-85) cc_final: 0.5049 (tpp80) REVERT: S 195 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6980 (mt-10) REVERT: S 200 ARG cc_start: 0.6335 (ttm-80) cc_final: 0.6051 (ttt-90) REVERT: S 206 MET cc_start: 0.5406 (mtt) cc_final: 0.5000 (tpp) REVERT: S 216 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6519 (tp30) REVERT: T 26 ASN cc_start: 0.8113 (t0) cc_final: 0.7880 (t0) REVERT: T 41 LYS cc_start: 0.8258 (mmtt) cc_final: 0.8035 (tppt) REVERT: T 111 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: T 175 LYS cc_start: 0.8009 (mttt) cc_final: 0.7779 (mtmt) REVERT: U 6 HIS cc_start: 0.7295 (p-80) cc_final: 0.7069 (p-80) REVERT: U 27 LYS cc_start: 0.8307 (tppt) cc_final: 0.8106 (mmtp) REVERT: U 55 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7595 (ptt-90) REVERT: U 58 GLU cc_start: 0.7736 (tp30) cc_final: 0.7526 (mm-30) REVERT: U 116 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8179 (tp30) REVERT: U 173 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7359 (mp0) REVERT: U 190 LYS cc_start: 0.8168 (mttt) cc_final: 0.7967 (mppt) REVERT: U 193 LYS cc_start: 0.7921 (tttt) cc_final: 0.7679 (ttmm) REVERT: U 204 ASP cc_start: 0.6331 (m-30) cc_final: 0.6047 (m-30) REVERT: U 217 LYS cc_start: 0.7406 (mttp) cc_final: 0.7161 (mmtm) REVERT: V 259 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7312 (ttm110) REVERT: V 280 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7722 (mtp85) REVERT: W 98 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7989 (mmpt) REVERT: W 260 GLU cc_start: 0.5258 (OUTLIER) cc_final: 0.4744 (mm-30) REVERT: W 274 THR cc_start: 0.7854 (OUTLIER) cc_final: 0.7475 (m) REVERT: W 281 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7715 (mm-30) REVERT: X 81 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8643 (mm-30) REVERT: X 115 ARG cc_start: 0.5714 (mtt180) cc_final: 0.5380 (mtm180) REVERT: X 132 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: X 149 MET cc_start: 0.7664 (mmm) cc_final: 0.7421 (mmm) REVERT: Y 50 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7991 (mp0) REVERT: Y 75 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.6139 (mtm110) REVERT: Y 78 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8232 (mtt-85) REVERT: Y 116 SER cc_start: 0.6003 (OUTLIER) cc_final: 0.5702 (m) REVERT: Y 188 LYS cc_start: 0.8078 (tptt) cc_final: 0.7877 (mptm) REVERT: Y 200 GLU cc_start: 0.7942 (pt0) cc_final: 0.7535 (pt0) REVERT: Z 117 HIS cc_start: 0.8675 (t-170) cc_final: 0.8473 (t-90) REVERT: Z 134 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7731 (tm130) REVERT: Z 177 GLU cc_start: 0.8533 (tt0) cc_final: 0.8300 (tt0) REVERT: Z 234 GLU cc_start: 0.8344 (pt0) cc_final: 0.8126 (mm-30) REVERT: a 105 GLN cc_start: 0.8611 (tt0) cc_final: 0.8269 (tp-100) REVERT: a 133 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7672 (tpt90) REVERT: a 242 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7812 (pm20) REVERT: b 1 MET cc_start: 0.6019 (mtm) cc_final: 0.5416 (tpt) REVERT: b 26 TYR cc_start: 0.8628 (t80) cc_final: 0.8379 (t80) REVERT: b 99 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8231 (tp30) REVERT: b 114 GLU cc_start: 0.7838 (tt0) cc_final: 0.7587 (tp30) REVERT: b 201 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8134 (mp0) REVERT: b 212 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8057 (mp0) outliers start: 299 outliers final: 94 residues processed: 1264 average time/residue: 1.5653 time to fit residues: 2383.0748 Evaluate side-chains 931 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 800 time to evaluate : 4.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 165 ARG Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 280 ARG Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 225 ASP Chi-restraints excluded: chain L residue 297 ILE Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 171 SER Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain M residue 177 PHE Chi-restraints excluded: chain M residue 189 GLN Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 234 ASP Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 175 ARG Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 115 ASP Chi-restraints excluded: chain Q residue 118 ARG Chi-restraints excluded: chain Q residue 221 LEU Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 62 SER Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 111 SER Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 157 ASP Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain S residue 196 THR Chi-restraints excluded: chain T residue 21 GLN Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 111 GLU Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain T residue 165 ARG Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 112 SER Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain V residue 75 SER Chi-restraints excluded: chain V residue 149 SER Chi-restraints excluded: chain V residue 164 SER Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 280 ARG Chi-restraints excluded: chain W residue 98 LYS Chi-restraints excluded: chain W residue 110 CYS Chi-restraints excluded: chain W residue 247 THR Chi-restraints excluded: chain W residue 260 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain Y residue 40 ASP Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Y residue 112 VAL Chi-restraints excluded: chain Y residue 116 SER Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Z residue 134 GLN Chi-restraints excluded: chain Z residue 141 VAL Chi-restraints excluded: chain Z residue 225 ASP Chi-restraints excluded: chain Z residue 297 ILE Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 133 ARG Chi-restraints excluded: chain a residue 171 SER Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 177 PHE Chi-restraints excluded: chain a residue 189 GLN Chi-restraints excluded: chain a residue 201 MET Chi-restraints excluded: chain a residue 234 ASP Chi-restraints excluded: chain b residue 212 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 515 optimal weight: 0.9990 chunk 462 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 247 optimal weight: 0.6980 chunk 478 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 290 optimal weight: 1.9990 chunk 355 optimal weight: 5.9990 chunk 553 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 166 HIS B 61 GLN B 121 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN C 65 ASN C 94 ASN C 108 GLN C 149 HIS D 97 ASN D 177 GLN E 41 GLN E 149 ASN E 168 GLN E 188 ASN E 232 GLN F 104 ASN G 216 ASN G 219 ASN G 223 GLN H 147 ASN H 196 ASN H 211 GLN J 201 ASN K 11 ASN K 143 HIS L 117 HIS L 139 GLN L 272 HIS L 302 GLN N 70 GLN N 71 GLN O 143 ASN O 166 HIS P 61 GLN P 121 GLN ** P 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 223 GLN Q 65 ASN Q 94 ASN Q 108 GLN R 97 ASN S 41 GLN S 149 ASN S 168 GLN S 188 ASN S 232 GLN T 104 ASN U 62 ASN U 216 ASN U 219 ASN U 223 GLN V 147 ASN V 196 ASN V 211 GLN X 201 ASN Y 11 ASN Y 143 HIS Z 117 HIS Z 139 GLN Z 272 HIS Z 302 GLN a 105 GLN b 70 GLN b 71 GLN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.143467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121593 restraints weight = 51666.633| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 0.98 r_work: 0.3299 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 49400 Z= 0.198 Angle : 0.635 8.384 66842 Z= 0.349 Chirality : 0.045 0.165 7506 Planarity : 0.005 0.062 8636 Dihedral : 8.229 71.717 7119 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.60 % Favored : 98.37 % Rotamer: Outliers : 3.31 % Allowed : 12.71 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.10), residues: 6194 helix: 0.53 (0.10), residues: 2334 sheet: 0.39 (0.13), residues: 1502 loop : -0.81 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 165 HIS 0.006 0.001 HIS Q 104 PHE 0.019 0.002 PHE M 134 TYR 0.026 0.002 TYR M 130 ARG 0.007 0.001 ARG N 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 891 time to evaluate : 4.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7437 (p0) cc_final: 0.7205 (p0) REVERT: A 114 ARG cc_start: 0.8251 (mmt-90) cc_final: 0.7998 (mmm-85) REVERT: A 178 ASN cc_start: 0.8184 (m-40) cc_final: 0.7945 (m-40) REVERT: A 196 LYS cc_start: 0.8071 (tttt) cc_final: 0.7731 (ttmt) REVERT: A 241 GLU cc_start: 0.6514 (pt0) cc_final: 0.6043 (pt0) REVERT: B 175 ARG cc_start: 0.6761 (mmm160) cc_final: 0.6451 (mtt-85) REVERT: B 178 ASN cc_start: 0.6875 (m-40) cc_final: 0.6651 (m110) REVERT: B 179 GLU cc_start: 0.6502 (mp0) cc_final: 0.6064 (mp0) REVERT: B 225 LYS cc_start: 0.6998 (ttmt) cc_final: 0.6690 (tptp) REVERT: C 4 ARG cc_start: 0.7059 (ptm-80) cc_final: 0.6817 (ptm-80) REVERT: C 8 ARG cc_start: 0.6524 (mtt-85) cc_final: 0.6212 (mtp85) REVERT: C 108 GLN cc_start: 0.8653 (mm110) cc_final: 0.8437 (mm110) REVERT: C 118 ARG cc_start: 0.7721 (mtp180) cc_final: 0.7387 (mtm110) REVERT: C 184 ASP cc_start: 0.6841 (m-30) cc_final: 0.6265 (t0) REVERT: D 15 HIS cc_start: 0.6376 (m170) cc_final: 0.6114 (m-70) REVERT: D 24 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7638 (mm-30) REVERT: D 105 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: D 143 HIS cc_start: 0.8066 (m170) cc_final: 0.7696 (m170) REVERT: D 171 PHE cc_start: 0.7504 (t80) cc_final: 0.7254 (t80) REVERT: D 187 HIS cc_start: 0.6632 (t70) cc_final: 0.6228 (t70) REVERT: D 217 MET cc_start: 0.5841 (ttp) cc_final: 0.5545 (ttp) REVERT: D 221 GLU cc_start: 0.5617 (tt0) cc_final: 0.5104 (tt0) REVERT: E 20 ARG cc_start: 0.7539 (mtt90) cc_final: 0.7190 (mtt90) REVERT: E 66 LYS cc_start: 0.7679 (mttp) cc_final: 0.7366 (mmmm) REVERT: E 119 LEU cc_start: 0.7742 (tp) cc_final: 0.7468 (tp) REVERT: E 122 ARG cc_start: 0.6593 (mtt90) cc_final: 0.6264 (mtp180) REVERT: E 152 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7810 (mt0) REVERT: E 184 ILE cc_start: 0.6109 (mt) cc_final: 0.5888 (mp) REVERT: E 216 GLU cc_start: 0.6338 (mt-10) cc_final: 0.5760 (tp30) REVERT: F 26 ASN cc_start: 0.7609 (t0) cc_final: 0.7365 (t0) REVERT: F 61 GLN cc_start: 0.6325 (OUTLIER) cc_final: 0.6095 (tp-100) REVERT: F 167 GLN cc_start: 0.7567 (tp40) cc_final: 0.7331 (tp-100) REVERT: F 231 ARG cc_start: 0.6583 (mtp85) cc_final: 0.6247 (mmm160) REVERT: G 5 GLU cc_start: 0.5795 (mt-10) cc_final: 0.5556 (tp30) REVERT: G 27 LYS cc_start: 0.7931 (tppt) cc_final: 0.7602 (mmtp) REVERT: G 196 HIS cc_start: 0.8033 (m-70) cc_final: 0.7788 (m90) REVERT: H 199 THR cc_start: 0.7170 (OUTLIER) cc_final: 0.6962 (m) REVERT: I 266 GLN cc_start: 0.6051 (tt0) cc_final: 0.5715 (tp-100) REVERT: I 281 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7162 (mm-30) REVERT: J 68 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7749 (mmt180) REVERT: J 132 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: J 134 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6838 (pm20) REVERT: J 192 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7137 (mtt-85) REVERT: K 1 MET cc_start: 0.5641 (mtm) cc_final: 0.5388 (ttm) REVERT: K 50 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7601 (mp0) REVERT: K 116 SER cc_start: 0.6153 (OUTLIER) cc_final: 0.5881 (m) REVERT: K 200 GLU cc_start: 0.7541 (pt0) cc_final: 0.7179 (pt0) REVERT: L 134 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.7073 (tm130) REVERT: L 251 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7522 (tp40) REVERT: L 304 LYS cc_start: 0.8095 (pttt) cc_final: 0.7843 (pttm) REVERT: M 105 GLN cc_start: 0.8269 (tt0) cc_final: 0.7951 (tp-100) REVERT: M 127 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8496 (t) REVERT: M 201 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7904 (mtp) REVERT: N 1 MET cc_start: 0.4763 (mtm) cc_final: 0.4449 (tpt) REVERT: N 97 GLN cc_start: 0.8131 (mm110) cc_final: 0.7921 (mp10) REVERT: O 43 ASP cc_start: 0.7406 (p0) cc_final: 0.7196 (p0) REVERT: O 114 ARG cc_start: 0.8269 (mmt-90) cc_final: 0.8016 (mmm-85) REVERT: O 178 ASN cc_start: 0.8184 (m-40) cc_final: 0.7944 (m-40) REVERT: O 196 LYS cc_start: 0.8069 (tttt) cc_final: 0.7734 (ttmt) REVERT: O 241 GLU cc_start: 0.6514 (pt0) cc_final: 0.6042 (pt0) REVERT: P 175 ARG cc_start: 0.6793 (mmm160) cc_final: 0.6196 (mmm-85) REVERT: P 178 ASN cc_start: 0.6896 (m-40) cc_final: 0.6656 (m110) REVERT: P 179 GLU cc_start: 0.6493 (mp0) cc_final: 0.6051 (mp0) REVERT: P 225 LYS cc_start: 0.7000 (ttmt) cc_final: 0.6681 (tptp) REVERT: Q 4 ARG cc_start: 0.7047 (ptm-80) cc_final: 0.6847 (ptm-80) REVERT: Q 8 ARG cc_start: 0.6537 (mtt-85) cc_final: 0.6225 (mtp85) REVERT: Q 108 GLN cc_start: 0.8656 (mm110) cc_final: 0.8441 (mm110) REVERT: Q 118 ARG cc_start: 0.7719 (mtp180) cc_final: 0.7414 (mtm110) REVERT: Q 184 ASP cc_start: 0.6845 (m-30) cc_final: 0.6273 (t0) REVERT: R 15 HIS cc_start: 0.6376 (m170) cc_final: 0.6112 (m-70) REVERT: R 24 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7629 (mm-30) REVERT: R 105 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: R 143 HIS cc_start: 0.8062 (m170) cc_final: 0.7694 (m170) REVERT: R 187 HIS cc_start: 0.6632 (t70) cc_final: 0.6228 (t70) REVERT: R 217 MET cc_start: 0.5845 (ttp) cc_final: 0.5546 (ttp) REVERT: R 221 GLU cc_start: 0.5610 (tt0) cc_final: 0.5104 (tt0) REVERT: S 20 ARG cc_start: 0.7535 (mtt90) cc_final: 0.7170 (mtt90) REVERT: S 66 LYS cc_start: 0.7676 (mttp) cc_final: 0.7361 (mmmm) REVERT: S 119 LEU cc_start: 0.7754 (tp) cc_final: 0.7479 (tp) REVERT: S 122 ARG cc_start: 0.6590 (mtt90) cc_final: 0.6261 (mtp180) REVERT: S 152 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7801 (mt0) REVERT: S 184 ILE cc_start: 0.6097 (mt) cc_final: 0.5879 (mp) REVERT: S 216 GLU cc_start: 0.6338 (mt-10) cc_final: 0.5757 (tp30) REVERT: T 26 ASN cc_start: 0.7608 (t0) cc_final: 0.7364 (t0) REVERT: T 61 GLN cc_start: 0.6314 (OUTLIER) cc_final: 0.6088 (tp-100) REVERT: T 167 GLN cc_start: 0.7574 (tp40) cc_final: 0.7340 (tp-100) REVERT: T 231 ARG cc_start: 0.6590 (mtp85) cc_final: 0.6248 (mmm160) REVERT: U 27 LYS cc_start: 0.7931 (tppt) cc_final: 0.7604 (mmtp) REVERT: U 196 HIS cc_start: 0.8044 (m-70) cc_final: 0.7813 (m90) REVERT: V 199 THR cc_start: 0.7167 (OUTLIER) cc_final: 0.6963 (m) REVERT: W 266 GLN cc_start: 0.6038 (tt0) cc_final: 0.5704 (tp-100) REVERT: W 281 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7193 (mm-30) REVERT: X 68 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7755 (mmt180) REVERT: X 132 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: X 134 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6870 (pm20) REVERT: X 192 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7125 (mtt-85) REVERT: Y 1 MET cc_start: 0.5655 (mtm) cc_final: 0.5400 (ttm) REVERT: Y 50 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7597 (mp0) REVERT: Y 116 SER cc_start: 0.6150 (OUTLIER) cc_final: 0.5870 (m) REVERT: Y 200 GLU cc_start: 0.7559 (pt0) cc_final: 0.7196 (pt0) REVERT: Z 134 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.7050 (tm130) REVERT: Z 251 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7518 (tp40) REVERT: Z 304 LYS cc_start: 0.8096 (pttt) cc_final: 0.7843 (pttm) REVERT: a 105 GLN cc_start: 0.8279 (tt0) cc_final: 0.7948 (tp-100) REVERT: a 201 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7900 (mtp) REVERT: b 1 MET cc_start: 0.4789 (mtm) cc_final: 0.4484 (tpt) REVERT: b 97 GLN cc_start: 0.8125 (mm110) cc_final: 0.7917 (mp10) outliers start: 171 outliers final: 60 residues processed: 989 average time/residue: 1.5681 time to fit residues: 1869.1455 Evaluate side-chains 828 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 745 time to evaluate : 4.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 192 ARG Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 251 GLN Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 234 ASP Chi-restraints excluded: chain N residue 189 SER Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 115 ASP Chi-restraints excluded: chain Q residue 161 ASN Chi-restraints excluded: chain Q residue 163 ASN Chi-restraints excluded: chain Q residue 229 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 62 SER Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 111 SER Chi-restraints excluded: chain S residue 152 GLN Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 196 THR Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain U residue 112 SER Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain W residue 247 THR Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 192 ARG Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Y residue 116 SER Chi-restraints excluded: chain Y residue 201 ILE Chi-restraints excluded: chain Z residue 134 GLN Chi-restraints excluded: chain Z residue 141 VAL Chi-restraints excluded: chain Z residue 251 GLN Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 201 MET Chi-restraints excluded: chain a residue 234 ASP Chi-restraints excluded: chain b residue 189 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 140 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 298 optimal weight: 6.9990 chunk 302 optimal weight: 2.9990 chunk 478 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 182 optimal weight: 0.0770 chunk 240 optimal weight: 5.9990 chunk 269 optimal weight: 9.9990 chunk 547 optimal weight: 3.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 143 ASN B 61 GLN B 121 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 94 ASN C 152 GLN C 175 GLN C 264 GLN E 149 ASN E 168 GLN F 26 ASN G 31 ASN G 62 ASN G 219 ASN H 147 ASN I 211 ASN I 266 GLN K 73 HIS L 180 ASN L 181 ASN L 233 HIS L 296 GLN L 302 GLN M 95 GLN M 105 GLN M 189 GLN O 52 ASN O 143 ASN P 61 GLN P 121 GLN ** P 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN Q 94 ASN Q 149 HIS Q 152 GLN Q 175 GLN Q 264 GLN S 149 ASN S 168 GLN T 26 ASN U 31 ASN U 62 ASN U 219 ASN V 147 ASN W 211 ASN W 266 GLN Y 73 HIS Z 180 ASN Z 233 HIS Z 296 GLN Z 302 GLN a 95 GLN a 189 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.141885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.119533 restraints weight = 51795.599| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.02 r_work: 0.3274 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 49400 Z= 0.317 Angle : 0.704 8.422 66842 Z= 0.383 Chirality : 0.049 0.177 7506 Planarity : 0.006 0.057 8636 Dihedral : 6.997 63.985 6949 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 4.06 % Allowed : 13.81 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 6194 helix: 1.17 (0.10), residues: 2334 sheet: 0.44 (0.13), residues: 1472 loop : -0.65 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 245 HIS 0.008 0.002 HIS S 91 PHE 0.029 0.003 PHE a 177 TYR 0.027 0.002 TYR F 117 ARG 0.006 0.001 ARG I 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 742 time to evaluate : 4.240 Fit side-chains REVERT: A 43 ASP cc_start: 0.7447 (p0) cc_final: 0.7200 (p0) REVERT: A 52 ASN cc_start: 0.6672 (t0) cc_final: 0.6315 (t0) REVERT: A 173 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7371 (mttp) REVERT: A 196 LYS cc_start: 0.8138 (tttt) cc_final: 0.7760 (ttmt) REVERT: A 241 GLU cc_start: 0.6633 (pt0) cc_final: 0.6117 (pt0) REVERT: B 90 LYS cc_start: 0.8641 (mtpm) cc_final: 0.8404 (mttp) REVERT: B 195 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6990 (tm-30) REVERT: C 8 ARG cc_start: 0.6437 (mtt-85) cc_final: 0.6130 (mtp85) REVERT: C 118 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7279 (mtm110) REVERT: C 142 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8402 (mm) REVERT: C 184 ASP cc_start: 0.6805 (m-30) cc_final: 0.6496 (t70) REVERT: C 215 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.6446 (mtm110) REVERT: D 15 HIS cc_start: 0.6210 (m170) cc_final: 0.5965 (m90) REVERT: D 24 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7581 (mm-30) REVERT: D 141 GLN cc_start: 0.6562 (tt0) cc_final: 0.6139 (tp40) REVERT: D 143 HIS cc_start: 0.8101 (m170) cc_final: 0.7748 (m170) REVERT: D 217 MET cc_start: 0.5808 (ttp) cc_final: 0.5426 (ttp) REVERT: E 10 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.5511 (mtp180) REVERT: E 66 LYS cc_start: 0.7687 (mttp) cc_final: 0.7387 (mmtm) REVERT: E 81 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7984 (mtt) REVERT: E 119 LEU cc_start: 0.7701 (tp) cc_final: 0.7375 (tp) REVERT: E 122 ARG cc_start: 0.6603 (mtt90) cc_final: 0.6160 (mtp180) REVERT: E 152 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7862 (mt0) REVERT: E 216 GLU cc_start: 0.6231 (mt-10) cc_final: 0.5630 (tp30) REVERT: F 26 ASN cc_start: 0.7920 (t0) cc_final: 0.7714 (t0) REVERT: F 167 GLN cc_start: 0.7613 (tp40) cc_final: 0.7249 (tp-100) REVERT: F 174 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6769 (mt-10) REVERT: G 5 GLU cc_start: 0.5814 (mt-10) cc_final: 0.5506 (mt-10) REVERT: G 178 ASN cc_start: 0.7481 (t0) cc_final: 0.7221 (t0) REVERT: G 196 HIS cc_start: 0.7973 (m-70) cc_final: 0.7729 (m90) REVERT: G 200 ASP cc_start: 0.5850 (t0) cc_final: 0.5644 (t0) REVERT: H 93 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: H 254 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.7952 (mttt) REVERT: H 282 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6018 (pt0) REVERT: I 266 GLN cc_start: 0.6315 (tt0) cc_final: 0.5803 (tp40) REVERT: J 68 ARG cc_start: 0.8220 (mtt-85) cc_final: 0.7891 (mmt180) REVERT: J 75 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8376 (mtpt) REVERT: J 134 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: J 192 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7071 (mtt-85) REVERT: K 28 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8079 (mtmm) REVERT: K 50 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7518 (mp0) REVERT: K 75 ARG cc_start: 0.5573 (mpt180) cc_final: 0.5319 (mpt90) REVERT: K 78 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7114 (mtp-110) REVERT: K 98 ASP cc_start: 0.7112 (m-30) cc_final: 0.6780 (p0) REVERT: K 116 SER cc_start: 0.6289 (OUTLIER) cc_final: 0.5933 (m) REVERT: K 200 GLU cc_start: 0.7450 (pt0) cc_final: 0.7188 (pt0) REVERT: L 134 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.7086 (tm130) REVERT: L 172 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: L 251 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7494 (tp40) REVERT: M 201 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7971 (mtp) REVERT: N 1 MET cc_start: 0.5234 (mtm) cc_final: 0.4840 (tpp) REVERT: N 212 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: O 43 ASP cc_start: 0.7441 (p0) cc_final: 0.7193 (p0) REVERT: O 52 ASN cc_start: 0.6679 (t0) cc_final: 0.6320 (t0) REVERT: O 173 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7369 (mttp) REVERT: O 196 LYS cc_start: 0.8141 (tttt) cc_final: 0.7761 (ttmt) REVERT: O 241 GLU cc_start: 0.6641 (pt0) cc_final: 0.6129 (pt0) REVERT: P 195 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7001 (tm-30) REVERT: Q 8 ARG cc_start: 0.6427 (mtt-85) cc_final: 0.6119 (mtp85) REVERT: Q 118 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7285 (mtm110) REVERT: Q 142 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8408 (mm) REVERT: Q 184 ASP cc_start: 0.6799 (m-30) cc_final: 0.6494 (t70) REVERT: Q 215 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.6429 (mtm110) REVERT: R 15 HIS cc_start: 0.6206 (m170) cc_final: 0.5964 (m90) REVERT: R 24 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7588 (mm-30) REVERT: R 60 ARG cc_start: 0.5556 (mtt180) cc_final: 0.5352 (mtp85) REVERT: R 141 GLN cc_start: 0.6555 (tt0) cc_final: 0.6124 (tp40) REVERT: R 143 HIS cc_start: 0.8104 (m170) cc_final: 0.7753 (m170) REVERT: R 217 MET cc_start: 0.5810 (ttp) cc_final: 0.5430 (ttp) REVERT: S 10 ARG cc_start: 0.6098 (OUTLIER) cc_final: 0.5501 (mtp180) REVERT: S 20 ARG cc_start: 0.7422 (mtt90) cc_final: 0.7078 (mtt90) REVERT: S 66 LYS cc_start: 0.7709 (mttp) cc_final: 0.7413 (mmtm) REVERT: S 81 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7990 (mtt) REVERT: S 119 LEU cc_start: 0.7704 (tp) cc_final: 0.7378 (tp) REVERT: S 122 ARG cc_start: 0.6597 (mtt90) cc_final: 0.6152 (mtp180) REVERT: S 152 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: S 216 GLU cc_start: 0.6237 (mt-10) cc_final: 0.5639 (tp30) REVERT: T 26 ASN cc_start: 0.7916 (t0) cc_final: 0.7704 (t0) REVERT: T 167 GLN cc_start: 0.7607 (tp40) cc_final: 0.7241 (tp-100) REVERT: T 174 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6791 (mt-10) REVERT: U 5 GLU cc_start: 0.5801 (mt-10) cc_final: 0.5502 (mt-10) REVERT: U 89 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7793 (tpt-90) REVERT: U 178 ASN cc_start: 0.7487 (t0) cc_final: 0.7228 (t0) REVERT: U 196 HIS cc_start: 0.7968 (m-70) cc_final: 0.7727 (m90) REVERT: U 200 ASP cc_start: 0.5856 (t0) cc_final: 0.5648 (t0) REVERT: V 93 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: V 254 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.7959 (mttt) REVERT: V 282 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6023 (pt0) REVERT: W 266 GLN cc_start: 0.6300 (tt0) cc_final: 0.5792 (tp40) REVERT: X 68 ARG cc_start: 0.8217 (mtt-85) cc_final: 0.7887 (mmt180) REVERT: X 75 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8382 (mtpt) REVERT: X 134 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7124 (pm20) REVERT: X 192 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7067 (mtt-85) REVERT: Y 28 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8080 (mtmm) REVERT: Y 50 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7518 (mp0) REVERT: Y 75 ARG cc_start: 0.5608 (mpt180) cc_final: 0.5361 (mpt90) REVERT: Y 78 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7121 (mtp-110) REVERT: Y 98 ASP cc_start: 0.7111 (m-30) cc_final: 0.6777 (p0) REVERT: Y 116 SER cc_start: 0.6287 (OUTLIER) cc_final: 0.5927 (m) REVERT: Y 200 GLU cc_start: 0.7457 (pt0) cc_final: 0.7176 (pt0) REVERT: Z 134 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7088 (tm130) REVERT: Z 172 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: Z 251 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7510 (tp40) REVERT: a 201 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7962 (mtp) REVERT: b 1 MET cc_start: 0.5216 (mtm) cc_final: 0.4828 (tpp) REVERT: b 212 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6818 (mp0) outliers start: 210 outliers final: 101 residues processed: 879 average time/residue: 1.5494 time to fit residues: 1644.6881 Evaluate side-chains 861 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 717 time to evaluate : 4.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 192 ARG Chi-restraints excluded: chain J residue 195 MET Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 78 ARG Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 172 GLU Chi-restraints excluded: chain L residue 251 GLN Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain M residue 189 GLN Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 238 SER Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain N residue 189 SER Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 173 LYS Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 115 ASP Chi-restraints excluded: chain Q residue 118 ARG Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 161 ASN Chi-restraints excluded: chain Q residue 163 ASN Chi-restraints excluded: chain Q residue 170 ILE Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 229 THR Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain S residue 10 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 81 MET Chi-restraints excluded: chain S residue 152 GLN Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 196 THR Chi-restraints excluded: chain S residue 217 ILE Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain S residue 233 THR Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain U residue 89 ARG Chi-restraints excluded: chain U residue 112 SER Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain V residue 93 GLU Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain V residue 208 CYS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 254 LYS Chi-restraints excluded: chain V residue 282 GLU Chi-restraints excluded: chain W residue 179 VAL Chi-restraints excluded: chain W residue 247 THR Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 192 ARG Chi-restraints excluded: chain X residue 195 MET Chi-restraints excluded: chain Y residue 28 LYS Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Y residue 78 ARG Chi-restraints excluded: chain Y residue 116 SER Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 201 ILE Chi-restraints excluded: chain Z residue 134 GLN Chi-restraints excluded: chain Z residue 141 VAL Chi-restraints excluded: chain Z residue 172 GLU Chi-restraints excluded: chain Z residue 251 GLN Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 189 GLN Chi-restraints excluded: chain a residue 201 MET Chi-restraints excluded: chain a residue 226 VAL Chi-restraints excluded: chain a residue 238 SER Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain b residue 189 SER Chi-restraints excluded: chain b residue 212 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 271 optimal weight: 0.8980 chunk 494 optimal weight: 6.9990 chunk 260 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 255 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 296 optimal weight: 2.9990 chunk 567 optimal weight: 3.9990 chunk 459 optimal weight: 1.9990 chunk 542 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN B 61 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 161 ASN E 149 ASN E 168 GLN F 61 GLN G 31 ASN G 62 ASN G 219 ASN H 147 ASN K 73 HIS L 139 GLN L 302 GLN M 189 GLN O 143 ASN P 61 GLN ** P 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN Q 161 ASN S 149 ASN S 168 GLN T 61 GLN U 31 ASN U 62 ASN U 219 ASN V 147 ASN Y 73 HIS Z 139 GLN Z 180 ASN Z 302 GLN a 105 GLN a 189 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.143292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.121121 restraints weight = 51724.316| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.01 r_work: 0.3296 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 49400 Z= 0.218 Angle : 0.594 8.311 66842 Z= 0.325 Chirality : 0.045 0.161 7506 Planarity : 0.005 0.057 8636 Dihedral : 6.407 68.112 6930 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.71 % Favored : 98.26 % Rotamer: Outliers : 3.91 % Allowed : 14.80 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.10), residues: 6194 helix: 1.67 (0.11), residues: 2342 sheet: 0.49 (0.13), residues: 1478 loop : -0.45 (0.12), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Z 165 HIS 0.005 0.001 HIS Q 104 PHE 0.023 0.002 PHE a 177 TYR 0.020 0.002 TYR M 130 ARG 0.005 0.001 ARG G 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 725 time to evaluate : 4.542 Fit side-chains REVERT: A 43 ASP cc_start: 0.7363 (p0) cc_final: 0.7120 (p0) REVERT: A 173 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7333 (mttp) REVERT: A 196 LYS cc_start: 0.8115 (tttt) cc_final: 0.7849 (tttp) REVERT: A 241 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6114 (pt0) REVERT: B 195 GLU cc_start: 0.7276 (mm-30) cc_final: 0.7013 (tm-30) REVERT: C 8 ARG cc_start: 0.6344 (mtt-85) cc_final: 0.6015 (mtp85) REVERT: C 118 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7313 (mtm110) REVERT: C 142 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8356 (mm) REVERT: C 184 ASP cc_start: 0.6775 (m-30) cc_final: 0.6476 (t70) REVERT: C 257 LEU cc_start: 0.6990 (mt) cc_final: 0.6773 (mt) REVERT: D 15 HIS cc_start: 0.6280 (m170) cc_final: 0.6025 (m-70) REVERT: D 24 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7516 (mm-30) REVERT: D 141 GLN cc_start: 0.6556 (tt0) cc_final: 0.6189 (tt0) REVERT: D 143 HIS cc_start: 0.8076 (m170) cc_final: 0.7704 (m170) REVERT: D 217 MET cc_start: 0.5833 (ttp) cc_final: 0.5488 (ttp) REVERT: E 10 ARG cc_start: 0.6095 (OUTLIER) cc_final: 0.5518 (mtp180) REVERT: E 66 LYS cc_start: 0.7707 (mttp) cc_final: 0.7429 (mmtm) REVERT: E 81 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7889 (mtt) REVERT: E 119 LEU cc_start: 0.7678 (tp) cc_final: 0.7392 (tp) REVERT: E 122 ARG cc_start: 0.6561 (mtt180) cc_final: 0.6138 (mtp180) REVERT: E 132 LEU cc_start: 0.5140 (OUTLIER) cc_final: 0.4416 (mp) REVERT: E 152 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: E 204 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6591 (tt0) REVERT: E 216 GLU cc_start: 0.6194 (mt-10) cc_final: 0.5518 (tp30) REVERT: F 26 ASN cc_start: 0.7833 (t0) cc_final: 0.7628 (t0) REVERT: F 61 GLN cc_start: 0.6295 (OUTLIER) cc_final: 0.5969 (tp-100) REVERT: F 167 GLN cc_start: 0.7638 (tp40) cc_final: 0.7258 (tp-100) REVERT: F 174 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6672 (mt-10) REVERT: G 171 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.7082 (mttp) REVERT: G 178 ASN cc_start: 0.7436 (t0) cc_final: 0.7181 (t0) REVERT: G 200 ASP cc_start: 0.5840 (t0) cc_final: 0.5622 (t0) REVERT: H 93 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: I 98 LYS cc_start: 0.7997 (mppt) cc_final: 0.7400 (mmpt) REVERT: J 68 ARG cc_start: 0.8183 (mtt-85) cc_final: 0.7880 (mmt180) REVERT: J 134 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7065 (pm20) REVERT: J 192 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7046 (mtt-85) REVERT: K 28 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7999 (mtmm) REVERT: K 50 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7487 (mp0) REVERT: K 75 ARG cc_start: 0.5529 (mpt180) cc_final: 0.5314 (mpt90) REVERT: K 78 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7280 (mtp-110) REVERT: K 200 GLU cc_start: 0.7415 (pt0) cc_final: 0.7179 (pt0) REVERT: L 134 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6996 (tm130) REVERT: L 251 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7480 (tp40) REVERT: N 1 MET cc_start: 0.5279 (mtm) cc_final: 0.4930 (tpp) REVERT: O 43 ASP cc_start: 0.7377 (p0) cc_final: 0.7136 (p0) REVERT: O 173 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7295 (mttp) REVERT: O 196 LYS cc_start: 0.8117 (tttt) cc_final: 0.7850 (tttp) REVERT: O 241 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6099 (pt0) REVERT: P 195 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7016 (tm-30) REVERT: Q 8 ARG cc_start: 0.6372 (mtt-85) cc_final: 0.6042 (mtp85) REVERT: Q 118 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7319 (mtm110) REVERT: Q 142 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8360 (mm) REVERT: Q 184 ASP cc_start: 0.6779 (m-30) cc_final: 0.6477 (t70) REVERT: Q 234 GLU cc_start: 0.7032 (mp0) cc_final: 0.6713 (mm-30) REVERT: Q 257 LEU cc_start: 0.6986 (mt) cc_final: 0.6765 (mt) REVERT: R 15 HIS cc_start: 0.6277 (m170) cc_final: 0.6025 (m-70) REVERT: R 24 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7534 (mm-30) REVERT: R 141 GLN cc_start: 0.6543 (tt0) cc_final: 0.6173 (tt0) REVERT: R 143 HIS cc_start: 0.8075 (m170) cc_final: 0.7703 (m170) REVERT: R 217 MET cc_start: 0.5828 (ttp) cc_final: 0.5488 (ttp) REVERT: S 10 ARG cc_start: 0.6082 (ptp-170) cc_final: 0.5509 (mtp180) REVERT: S 20 ARG cc_start: 0.7455 (mtt90) cc_final: 0.7084 (mtt90) REVERT: S 66 LYS cc_start: 0.7708 (mttp) cc_final: 0.7429 (mmtm) REVERT: S 81 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7867 (mtt) REVERT: S 119 LEU cc_start: 0.7682 (tp) cc_final: 0.7396 (tp) REVERT: S 122 ARG cc_start: 0.6552 (mtt180) cc_final: 0.6130 (mtp180) REVERT: S 132 LEU cc_start: 0.5158 (OUTLIER) cc_final: 0.4430 (mp) REVERT: S 152 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7829 (mt0) REVERT: S 204 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6591 (tt0) REVERT: S 216 GLU cc_start: 0.6205 (mt-10) cc_final: 0.5533 (tp30) REVERT: T 26 ASN cc_start: 0.7831 (t0) cc_final: 0.7624 (t0) REVERT: T 61 GLN cc_start: 0.6282 (OUTLIER) cc_final: 0.5955 (tp-100) REVERT: T 167 GLN cc_start: 0.7640 (tp40) cc_final: 0.7259 (tp-100) REVERT: T 174 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6686 (mt-10) REVERT: U 89 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7701 (tpt-90) REVERT: U 178 ASN cc_start: 0.7438 (t0) cc_final: 0.7188 (t0) REVERT: U 200 ASP cc_start: 0.5859 (t0) cc_final: 0.5637 (t0) REVERT: V 93 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: W 98 LYS cc_start: 0.7998 (mppt) cc_final: 0.7407 (mmpt) REVERT: X 68 ARG cc_start: 0.8183 (mtt-85) cc_final: 0.7878 (mmt180) REVERT: X 134 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7068 (pm20) REVERT: X 192 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7047 (mtt-85) REVERT: Y 28 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8000 (mtmm) REVERT: Y 50 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7481 (mp0) REVERT: Y 78 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7268 (mtp-110) REVERT: Y 200 GLU cc_start: 0.7445 (pt0) cc_final: 0.7196 (pt0) REVERT: Z 134 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6997 (tm130) REVERT: Z 251 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7470 (tp40) REVERT: b 1 MET cc_start: 0.5267 (mtm) cc_final: 0.4922 (tpp) outliers start: 202 outliers final: 78 residues processed: 851 average time/residue: 1.5501 time to fit residues: 1595.2852 Evaluate side-chains 798 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 683 time to evaluate : 4.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 192 ARG Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 78 ARG Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 139 GLN Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 251 GLN Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain N residue 189 SER Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 173 LYS Chi-restraints excluded: chain O residue 241 GLU Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 115 ASP Chi-restraints excluded: chain Q residue 118 ARG Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 161 ASN Chi-restraints excluded: chain Q residue 170 ILE Chi-restraints excluded: chain Q residue 229 THR Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 81 MET Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 152 GLN Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 196 THR Chi-restraints excluded: chain S residue 204 GLN Chi-restraints excluded: chain S residue 228 GLU Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain S residue 233 THR Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain U residue 89 ARG Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain V residue 93 GLU Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain W residue 247 THR Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 192 ARG Chi-restraints excluded: chain Y residue 28 LYS Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 78 ARG Chi-restraints excluded: chain Y residue 201 ILE Chi-restraints excluded: chain Z residue 134 GLN Chi-restraints excluded: chain Z residue 139 GLN Chi-restraints excluded: chain Z residue 141 VAL Chi-restraints excluded: chain Z residue 251 GLN Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain b residue 189 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 358 optimal weight: 0.8980 chunk 511 optimal weight: 0.9980 chunk 291 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 315 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 507 optimal weight: 0.0050 chunk 430 optimal weight: 5.9990 chunk 478 optimal weight: 0.8980 chunk 400 optimal weight: 9.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN B 61 GLN B 187 HIS C 94 ASN E 149 ASN E 168 GLN F 61 GLN G 62 ASN G 196 HIS G 219 ASN H 147 ASN I 266 GLN L 180 ASN L 302 GLN O 143 ASN P 61 GLN P 187 HIS Q 94 ASN S 149 ASN S 168 GLN T 61 GLN U 62 ASN U 196 HIS U 219 ASN V 147 ASN W 266 GLN Y 73 HIS Z 180 ASN Z 302 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.145629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123943 restraints weight = 51833.899| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.09 r_work: 0.3330 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 49400 Z= 0.144 Angle : 0.518 7.811 66842 Z= 0.283 Chirality : 0.042 0.155 7506 Planarity : 0.004 0.054 8636 Dihedral : 5.837 71.074 6916 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.61 % Favored : 98.35 % Rotamer: Outliers : 2.80 % Allowed : 15.86 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.10), residues: 6194 helix: 2.10 (0.11), residues: 2350 sheet: 0.50 (0.13), residues: 1482 loop : -0.28 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 165 HIS 0.004 0.001 HIS B 187 PHE 0.017 0.001 PHE a 177 TYR 0.017 0.001 TYR a 130 ARG 0.005 0.000 ARG Q 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 772 time to evaluate : 4.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8073 (tttt) cc_final: 0.7662 (ttmt) REVERT: A 241 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6062 (pt0) REVERT: B 195 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7021 (tm-30) REVERT: C 8 ARG cc_start: 0.6300 (mtt-85) cc_final: 0.5955 (mtp85) REVERT: C 115 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7526 (m-30) REVERT: C 118 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7304 (mtm110) REVERT: C 142 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8360 (mm) REVERT: C 165 TRP cc_start: 0.8352 (m100) cc_final: 0.8046 (m100) REVERT: C 166 ARG cc_start: 0.8053 (mtt-85) cc_final: 0.7531 (mtp180) REVERT: C 178 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6675 (tt0) REVERT: C 184 ASP cc_start: 0.6769 (m-30) cc_final: 0.6493 (t70) REVERT: C 215 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7108 (mmm-85) REVERT: C 257 LEU cc_start: 0.7011 (mt) cc_final: 0.6777 (mt) REVERT: D 4 ASP cc_start: 0.6789 (OUTLIER) cc_final: 0.6503 (t0) REVERT: D 15 HIS cc_start: 0.6326 (m170) cc_final: 0.6062 (m-70) REVERT: D 24 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7482 (mm-30) REVERT: D 61 LYS cc_start: 0.7054 (mmtp) cc_final: 0.6396 (mptt) REVERT: D 143 HIS cc_start: 0.8039 (m170) cc_final: 0.7655 (OUTLIER) REVERT: D 217 MET cc_start: 0.5806 (ttp) cc_final: 0.5472 (ttp) REVERT: E 10 ARG cc_start: 0.6053 (ptp-170) cc_final: 0.5467 (mtp180) REVERT: E 20 ARG cc_start: 0.7458 (mtt90) cc_final: 0.7108 (mtt90) REVERT: E 66 LYS cc_start: 0.7685 (mttp) cc_final: 0.7393 (mmtm) REVERT: E 119 LEU cc_start: 0.7635 (tp) cc_final: 0.7403 (tp) REVERT: E 122 ARG cc_start: 0.6558 (mtt180) cc_final: 0.6356 (mtp180) REVERT: E 132 LEU cc_start: 0.5100 (OUTLIER) cc_final: 0.4414 (mp) REVERT: E 152 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7782 (mt0) REVERT: E 204 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6442 (tt0) REVERT: E 216 GLU cc_start: 0.6240 (mt-10) cc_final: 0.5614 (tp30) REVERT: F 26 ASN cc_start: 0.7672 (t0) cc_final: 0.7448 (t0) REVERT: F 167 GLN cc_start: 0.7616 (tp40) cc_final: 0.7300 (tp-100) REVERT: F 174 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6669 (mt-10) REVERT: F 231 ARG cc_start: 0.6441 (mtp85) cc_final: 0.6212 (mmm160) REVERT: G 171 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.7075 (mttp) REVERT: G 200 ASP cc_start: 0.5845 (t0) cc_final: 0.5621 (t0) REVERT: H 93 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: I 98 LYS cc_start: 0.7979 (mppt) cc_final: 0.7398 (mmpt) REVERT: J 68 ARG cc_start: 0.8205 (mtt-85) cc_final: 0.7905 (mmt180) REVERT: J 132 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: J 134 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6988 (pm20) REVERT: J 192 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6980 (mtt-85) REVERT: K 28 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7969 (mtmm) REVERT: K 50 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7467 (mp0) REVERT: K 78 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7132 (mtp-110) REVERT: K 200 GLU cc_start: 0.7453 (pt0) cc_final: 0.7135 (pt0) REVERT: L 134 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6855 (tm130) REVERT: L 251 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7471 (tp40) REVERT: N 1 MET cc_start: 0.5196 (mtm) cc_final: 0.4892 (tpp) REVERT: O 196 LYS cc_start: 0.8072 (tttt) cc_final: 0.7658 (ttmt) REVERT: O 241 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6061 (pt0) REVERT: P 195 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7016 (tm-30) REVERT: Q 8 ARG cc_start: 0.6314 (mtt-85) cc_final: 0.5967 (mtp85) REVERT: Q 115 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7522 (m-30) REVERT: Q 118 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7291 (mtm110) REVERT: Q 142 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8363 (mm) REVERT: Q 166 ARG cc_start: 0.8048 (mtt-85) cc_final: 0.7520 (mtp180) REVERT: Q 178 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6664 (tt0) REVERT: Q 184 ASP cc_start: 0.6760 (m-30) cc_final: 0.6485 (t70) REVERT: Q 215 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7114 (mmm-85) REVERT: Q 257 LEU cc_start: 0.7004 (mt) cc_final: 0.6769 (mt) REVERT: R 4 ASP cc_start: 0.6805 (OUTLIER) cc_final: 0.6518 (t0) REVERT: R 15 HIS cc_start: 0.6309 (m170) cc_final: 0.6047 (m-70) REVERT: R 24 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7498 (mm-30) REVERT: R 61 LYS cc_start: 0.7056 (mmtp) cc_final: 0.6395 (mptt) REVERT: R 143 HIS cc_start: 0.8043 (m170) cc_final: 0.7659 (OUTLIER) REVERT: R 217 MET cc_start: 0.5866 (ttp) cc_final: 0.5541 (ttp) REVERT: S 10 ARG cc_start: 0.6049 (OUTLIER) cc_final: 0.5484 (mtp180) REVERT: S 20 ARG cc_start: 0.7476 (mtt90) cc_final: 0.7127 (mtt90) REVERT: S 66 LYS cc_start: 0.7689 (mttp) cc_final: 0.7400 (mmtm) REVERT: S 119 LEU cc_start: 0.7640 (tp) cc_final: 0.7306 (tp) REVERT: S 122 ARG cc_start: 0.6554 (mtt180) cc_final: 0.6249 (mtp180) REVERT: S 132 LEU cc_start: 0.5099 (OUTLIER) cc_final: 0.4411 (mp) REVERT: S 152 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7797 (mt0) REVERT: S 204 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6447 (tt0) REVERT: S 216 GLU cc_start: 0.6247 (mt-10) cc_final: 0.5621 (tp30) REVERT: T 26 ASN cc_start: 0.7680 (t0) cc_final: 0.7454 (t0) REVERT: T 167 GLN cc_start: 0.7607 (tp40) cc_final: 0.7288 (tp-100) REVERT: T 174 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6674 (mt-10) REVERT: U 200 ASP cc_start: 0.5828 (t0) cc_final: 0.5609 (t0) REVERT: V 93 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7232 (tm-30) REVERT: W 98 LYS cc_start: 0.7990 (mppt) cc_final: 0.7405 (mmpt) REVERT: X 68 ARG cc_start: 0.8208 (mtt-85) cc_final: 0.7907 (mmt180) REVERT: X 132 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: X 134 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6995 (pm20) REVERT: X 192 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6982 (mtt-85) REVERT: Y 28 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7989 (mtmm) REVERT: Y 50 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7467 (mp0) REVERT: Y 75 ARG cc_start: 0.5681 (mpt180) cc_final: 0.5149 (mpt90) REVERT: Y 78 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7158 (mtp-110) REVERT: Y 200 GLU cc_start: 0.7460 (pt0) cc_final: 0.7142 (pt0) REVERT: Z 134 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6859 (tm130) REVERT: Z 251 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7465 (tp40) REVERT: b 1 MET cc_start: 0.5183 (mtm) cc_final: 0.4870 (tpp) outliers start: 145 outliers final: 45 residues processed: 849 average time/residue: 1.5392 time to fit residues: 1581.3806 Evaluate side-chains 796 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 713 time to evaluate : 4.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 192 ARG Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 78 ARG Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 251 GLN Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain N residue 189 SER Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 241 GLU Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 175 ARG Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 115 ASP Chi-restraints excluded: chain Q residue 118 ARG Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 178 GLN Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 229 THR Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain S residue 10 ARG Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 152 GLN Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 204 GLN Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain V residue 93 GLU Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 192 ARG Chi-restraints excluded: chain Y residue 28 LYS Chi-restraints excluded: chain Y residue 78 ARG Chi-restraints excluded: chain Z residue 134 GLN Chi-restraints excluded: chain Z residue 141 VAL Chi-restraints excluded: chain Z residue 251 GLN Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain b residue 189 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 579 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 279 optimal weight: 6.9990 chunk 500 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 478 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN B 187 HIS C 94 ASN ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN E 149 ASN G 62 ASN G 178 ASN G 196 HIS G 219 ASN H 147 ASN I 266 GLN K 73 HIS L 139 GLN L 302 GLN O 93 GLN O 143 ASN P 187 HIS Q 94 ASN Q 161 ASN S 149 ASN U 62 ASN U 178 ASN U 196 HIS U 219 ASN V 147 ASN W 266 GLN Z 139 GLN Z 180 ASN Z 302 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.144786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122904 restraints weight = 51779.247| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.05 r_work: 0.3319 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 49400 Z= 0.174 Angle : 0.541 8.018 66842 Z= 0.295 Chirality : 0.043 0.152 7506 Planarity : 0.004 0.053 8636 Dihedral : 5.842 69.875 6908 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.70 % Favored : 98.27 % Rotamer: Outliers : 3.38 % Allowed : 15.69 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.10), residues: 6194 helix: 2.14 (0.11), residues: 2350 sheet: 0.61 (0.13), residues: 1464 loop : -0.27 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 165 HIS 0.004 0.001 HIS U 196 PHE 0.018 0.002 PHE a 177 TYR 0.018 0.001 TYR a 130 ARG 0.004 0.000 ARG U 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 721 time to evaluate : 4.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8092 (tttt) cc_final: 0.7678 (ttmt) REVERT: A 241 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6126 (pt0) REVERT: B 195 GLU cc_start: 0.7246 (mm-30) cc_final: 0.7004 (tm-30) REVERT: C 8 ARG cc_start: 0.6267 (mtt-85) cc_final: 0.5912 (mtp85) REVERT: C 63 ASP cc_start: 0.7761 (t0) cc_final: 0.7361 (t0) REVERT: C 115 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: C 118 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7313 (mtm110) REVERT: C 142 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8381 (mm) REVERT: C 165 TRP cc_start: 0.8355 (m100) cc_final: 0.8084 (m100) REVERT: C 178 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6734 (tt0) REVERT: C 184 ASP cc_start: 0.6800 (m-30) cc_final: 0.6501 (t70) REVERT: D 4 ASP cc_start: 0.6724 (OUTLIER) cc_final: 0.6442 (t0) REVERT: D 15 HIS cc_start: 0.6333 (m170) cc_final: 0.6062 (m90) REVERT: D 24 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7466 (mm-30) REVERT: D 61 LYS cc_start: 0.7050 (mmtp) cc_final: 0.6393 (mptt) REVERT: D 143 HIS cc_start: 0.8066 (m170) cc_final: 0.7680 (OUTLIER) REVERT: D 206 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7560 (tt) REVERT: D 217 MET cc_start: 0.5820 (ttp) cc_final: 0.5505 (ttp) REVERT: E 10 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5467 (mtp180) REVERT: E 66 LYS cc_start: 0.7716 (mttp) cc_final: 0.7455 (mmtm) REVERT: E 119 LEU cc_start: 0.7677 (tp) cc_final: 0.7359 (tp) REVERT: E 122 ARG cc_start: 0.6557 (mtt180) cc_final: 0.6254 (mtp180) REVERT: E 132 LEU cc_start: 0.5173 (OUTLIER) cc_final: 0.4472 (mp) REVERT: E 216 GLU cc_start: 0.6261 (mt-10) cc_final: 0.5586 (tp30) REVERT: F 26 ASN cc_start: 0.7793 (t0) cc_final: 0.7568 (t0) REVERT: F 174 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6654 (mt-10) REVERT: G 200 ASP cc_start: 0.5818 (t0) cc_final: 0.5599 (t0) REVERT: H 93 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: H 282 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.6261 (pt0) REVERT: I 98 LYS cc_start: 0.7982 (mppt) cc_final: 0.7387 (mmpt) REVERT: J 68 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.7918 (mmt180) REVERT: J 132 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: J 134 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7045 (pm20) REVERT: J 192 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6951 (mtt-85) REVERT: K 28 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7951 (mtmm) REVERT: K 50 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7474 (mp0) REVERT: K 200 GLU cc_start: 0.7451 (pt0) cc_final: 0.7149 (pt0) REVERT: L 134 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6880 (tm130) REVERT: L 251 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7486 (tp40) REVERT: O 196 LYS cc_start: 0.8099 (tttt) cc_final: 0.7682 (ttmt) REVERT: O 241 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6136 (pt0) REVERT: P 195 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6998 (tm-30) REVERT: Q 8 ARG cc_start: 0.6268 (mtt-85) cc_final: 0.5907 (mtp85) REVERT: Q 63 ASP cc_start: 0.7766 (t0) cc_final: 0.7369 (t0) REVERT: Q 115 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: Q 118 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7311 (mtm110) REVERT: Q 142 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8379 (mm) REVERT: Q 165 TRP cc_start: 0.8353 (m100) cc_final: 0.8082 (m100) REVERT: Q 178 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6729 (tt0) REVERT: Q 184 ASP cc_start: 0.6800 (m-30) cc_final: 0.6498 (t70) REVERT: R 4 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6556 (t0) REVERT: R 15 HIS cc_start: 0.6333 (m170) cc_final: 0.6064 (m90) REVERT: R 24 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7477 (mm-30) REVERT: R 61 LYS cc_start: 0.7065 (mmtp) cc_final: 0.6415 (mptt) REVERT: R 143 HIS cc_start: 0.8061 (m170) cc_final: 0.7679 (OUTLIER) REVERT: R 206 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7556 (tt) REVERT: R 217 MET cc_start: 0.5823 (ttp) cc_final: 0.5528 (ttp) REVERT: S 10 ARG cc_start: 0.6025 (OUTLIER) cc_final: 0.5467 (mtp180) REVERT: S 20 ARG cc_start: 0.7508 (mtt90) cc_final: 0.7141 (mtt90) REVERT: S 66 LYS cc_start: 0.7715 (mttp) cc_final: 0.7453 (mmtm) REVERT: S 119 LEU cc_start: 0.7681 (tp) cc_final: 0.7364 (tp) REVERT: S 122 ARG cc_start: 0.6551 (mtt180) cc_final: 0.6255 (mtp180) REVERT: S 132 LEU cc_start: 0.5175 (OUTLIER) cc_final: 0.4468 (mp) REVERT: S 216 GLU cc_start: 0.6276 (mt-10) cc_final: 0.5597 (tp30) REVERT: T 26 ASN cc_start: 0.7797 (t0) cc_final: 0.7564 (t0) REVERT: T 174 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6669 (mt-10) REVERT: U 89 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7630 (tpt170) REVERT: U 200 ASP cc_start: 0.5813 (t0) cc_final: 0.5596 (t0) REVERT: V 93 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: V 282 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6048 (pt0) REVERT: W 98 LYS cc_start: 0.7996 (mppt) cc_final: 0.7392 (mmpt) REVERT: X 68 ARG cc_start: 0.8209 (mtt-85) cc_final: 0.7907 (mmt180) REVERT: X 132 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: X 134 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7035 (pm20) REVERT: X 192 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6944 (mtt-85) REVERT: Y 28 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7956 (mtmm) REVERT: Y 50 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7430 (mp0) REVERT: Y 70 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6571 (ttp) REVERT: Y 75 ARG cc_start: 0.5565 (mpt180) cc_final: 0.5051 (mpt90) REVERT: Y 78 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7123 (mtp-110) REVERT: Y 200 GLU cc_start: 0.7450 (pt0) cc_final: 0.7152 (pt0) REVERT: Z 134 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6876 (tm130) REVERT: Z 251 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7481 (tp40) outliers start: 175 outliers final: 69 residues processed: 823 average time/residue: 1.5600 time to fit residues: 1551.1706 Evaluate side-chains 813 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 707 time to evaluate : 4.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 192 ARG Chi-restraints excluded: chain J residue 195 MET Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 139 GLN Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 251 GLN Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain N residue 189 SER Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 241 GLU Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 231 ILE Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 115 ASP Chi-restraints excluded: chain Q residue 118 ARG Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 170 ILE Chi-restraints excluded: chain Q residue 178 GLN Chi-restraints excluded: chain Q residue 192 ASP Chi-restraints excluded: chain Q residue 229 THR Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain S residue 10 ARG Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 228 GLU Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain S residue 233 THR Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain U residue 89 ARG Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain V residue 93 GLU Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 282 GLU Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 192 ARG Chi-restraints excluded: chain X residue 195 MET Chi-restraints excluded: chain Y residue 28 LYS Chi-restraints excluded: chain Y residue 70 MET Chi-restraints excluded: chain Y residue 78 ARG Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 187 ASP Chi-restraints excluded: chain Z residue 134 GLN Chi-restraints excluded: chain Z residue 139 GLN Chi-restraints excluded: chain Z residue 141 VAL Chi-restraints excluded: chain Z residue 251 GLN Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain b residue 189 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 94 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 423 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 594 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 442 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 498 optimal weight: 10.0000 chunk 451 optimal weight: 10.0000 chunk 153 optimal weight: 0.9980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 143 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN C 175 GLN D 97 ASN E 149 ASN F 167 GLN G 62 ASN G 178 ASN G 196 HIS G 219 ASN H 147 ASN K 73 HIS L 139 GLN L 180 ASN L 302 GLN O 93 GLN O 143 ASN P 187 HIS Q 94 ASN Q 161 ASN Q 175 GLN R 97 ASN S 149 ASN T 167 GLN U 62 ASN U 178 ASN U 196 HIS U 219 ASN V 147 ASN Y 73 HIS Z 139 GLN Z 180 ASN Z 302 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121095 restraints weight = 51572.094| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.07 r_work: 0.3289 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 49400 Z= 0.275 Angle : 0.639 8.477 66842 Z= 0.347 Chirality : 0.046 0.170 7506 Planarity : 0.005 0.063 8636 Dihedral : 6.162 66.625 6902 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.97 % Rotamer: Outliers : 3.40 % Allowed : 15.42 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.10), residues: 6194 helix: 1.90 (0.11), residues: 2342 sheet: 0.61 (0.13), residues: 1482 loop : -0.40 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Z 165 HIS 0.005 0.001 HIS Q 104 PHE 0.021 0.002 PHE a 177 TYR 0.022 0.002 TYR F 117 ARG 0.009 0.001 ARG M 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 712 time to evaluate : 4.461 Fit side-chains REVERT: A 173 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7291 (mttp) REVERT: A 196 LYS cc_start: 0.8160 (tttt) cc_final: 0.7751 (ttmt) REVERT: B 183 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5916 (tt0) REVERT: B 195 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7059 (tm-30) REVERT: C 8 ARG cc_start: 0.6283 (mtt-85) cc_final: 0.5943 (mtp85) REVERT: C 115 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: C 118 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7329 (mtm110) REVERT: C 142 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8361 (mm) REVERT: C 178 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6767 (tt0) REVERT: C 184 ASP cc_start: 0.6918 (m-30) cc_final: 0.6589 (t70) REVERT: D 15 HIS cc_start: 0.6238 (m170) cc_final: 0.5984 (m90) REVERT: D 24 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7513 (mm-30) REVERT: D 141 GLN cc_start: 0.6628 (tt0) cc_final: 0.6119 (tp-100) REVERT: D 143 HIS cc_start: 0.8099 (m170) cc_final: 0.7744 (m170) REVERT: D 206 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7564 (tt) REVERT: D 217 MET cc_start: 0.5796 (ttp) cc_final: 0.5474 (ttp) REVERT: E 10 ARG cc_start: 0.6025 (OUTLIER) cc_final: 0.5458 (mtp180) REVERT: E 66 LYS cc_start: 0.7708 (mttp) cc_final: 0.7430 (mmtm) REVERT: E 119 LEU cc_start: 0.7715 (tp) cc_final: 0.7426 (tp) REVERT: E 122 ARG cc_start: 0.6587 (mtt180) cc_final: 0.6165 (mtp180) REVERT: E 132 LEU cc_start: 0.5269 (OUTLIER) cc_final: 0.4599 (mp) REVERT: E 152 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7798 (mt0) REVERT: E 216 GLU cc_start: 0.6360 (mt-10) cc_final: 0.5675 (tp30) REVERT: F 167 GLN cc_start: 0.7637 (tp40) cc_final: 0.7298 (tp-100) REVERT: F 174 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6760 (mt-10) REVERT: G 200 ASP cc_start: 0.5821 (t0) cc_final: 0.5598 (t0) REVERT: H 93 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: H 282 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6001 (pt0) REVERT: I 98 LYS cc_start: 0.8030 (mppt) cc_final: 0.7442 (mmpt) REVERT: J 68 ARG cc_start: 0.8245 (mtt-85) cc_final: 0.7919 (mmt180) REVERT: J 134 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7053 (pm20) REVERT: J 192 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6976 (mtt-85) REVERT: K 1 MET cc_start: 0.5131 (ttm) cc_final: 0.4741 (mmm) REVERT: K 28 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8015 (mtmm) REVERT: K 50 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7435 (mp0) REVERT: K 98 ASP cc_start: 0.7143 (m-30) cc_final: 0.6795 (p0) REVERT: K 116 SER cc_start: 0.6337 (p) cc_final: 0.6023 (m) REVERT: K 200 GLU cc_start: 0.7547 (pt0) cc_final: 0.7197 (pt0) REVERT: L 134 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6310 (tm-30) REVERT: L 163 GLN cc_start: 0.8152 (mt0) cc_final: 0.7944 (mt0) REVERT: L 251 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7504 (tp40) REVERT: O 173 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7321 (mttp) REVERT: O 196 LYS cc_start: 0.8155 (tttt) cc_final: 0.7742 (ttmt) REVERT: O 241 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6148 (pt0) REVERT: P 195 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7055 (tm-30) REVERT: Q 8 ARG cc_start: 0.6290 (mtt-85) cc_final: 0.5947 (mtp85) REVERT: Q 115 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: Q 118 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7355 (mtm110) REVERT: Q 142 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8361 (mm) REVERT: Q 178 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6764 (tt0) REVERT: Q 184 ASP cc_start: 0.6920 (m-30) cc_final: 0.6572 (t70) REVERT: R 15 HIS cc_start: 0.6238 (m170) cc_final: 0.5985 (m90) REVERT: R 24 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7516 (mm-30) REVERT: R 141 GLN cc_start: 0.6615 (tt0) cc_final: 0.6106 (tp-100) REVERT: R 143 HIS cc_start: 0.8094 (m170) cc_final: 0.7743 (m170) REVERT: R 206 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7563 (tt) REVERT: R 217 MET cc_start: 0.5846 (ttp) cc_final: 0.5528 (ttp) REVERT: S 10 ARG cc_start: 0.6058 (OUTLIER) cc_final: 0.5518 (mtp180) REVERT: S 66 LYS cc_start: 0.7705 (mttp) cc_final: 0.7430 (mmtm) REVERT: S 119 LEU cc_start: 0.7719 (tp) cc_final: 0.7431 (tp) REVERT: S 122 ARG cc_start: 0.6579 (mtt180) cc_final: 0.6156 (mtp180) REVERT: S 132 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.4579 (mp) REVERT: S 152 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: S 216 GLU cc_start: 0.6366 (mt-10) cc_final: 0.5660 (tp30) REVERT: T 167 GLN cc_start: 0.7636 (tp40) cc_final: 0.7293 (tp-100) REVERT: T 174 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6754 (mt-10) REVERT: T 231 ARG cc_start: 0.6325 (mmm160) cc_final: 0.5353 (tpm-80) REVERT: U 89 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7760 (tpt-90) REVERT: U 200 ASP cc_start: 0.5830 (t0) cc_final: 0.5612 (t0) REVERT: V 93 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: V 282 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6012 (pt0) REVERT: W 98 LYS cc_start: 0.8031 (mppt) cc_final: 0.7440 (mmpt) REVERT: X 68 ARG cc_start: 0.8241 (mtt-85) cc_final: 0.7915 (mmt180) REVERT: X 134 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7051 (pm20) REVERT: X 192 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6967 (mtt-85) REVERT: Y 1 MET cc_start: 0.5142 (ttm) cc_final: 0.4766 (mmm) REVERT: Y 28 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8014 (mtmm) REVERT: Y 50 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7433 (mp0) REVERT: Y 75 ARG cc_start: 0.5660 (mpt180) cc_final: 0.5147 (mpt90) REVERT: Y 98 ASP cc_start: 0.7132 (m-30) cc_final: 0.6805 (p0) REVERT: Y 116 SER cc_start: 0.6393 (p) cc_final: 0.6022 (m) REVERT: Y 200 GLU cc_start: 0.7546 (pt0) cc_final: 0.7200 (pt0) REVERT: Z 134 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.6310 (tm-30) REVERT: Z 163 GLN cc_start: 0.8174 (mt0) cc_final: 0.7967 (mt0) REVERT: Z 251 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7509 (tp40) outliers start: 176 outliers final: 86 residues processed: 822 average time/residue: 1.5494 time to fit residues: 1541.3056 Evaluate side-chains 810 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 687 time to evaluate : 4.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 192 ARG Chi-restraints excluded: chain J residue 195 MET Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 139 GLN Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 251 GLN Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 234 ASP Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain N residue 189 SER Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 173 LYS Chi-restraints excluded: chain O residue 241 GLU Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 115 ASP Chi-restraints excluded: chain Q residue 118 ARG Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 161 ASN Chi-restraints excluded: chain Q residue 178 GLN Chi-restraints excluded: chain Q residue 192 ASP Chi-restraints excluded: chain Q residue 229 THR Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain S residue 10 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 133 MET Chi-restraints excluded: chain S residue 152 GLN Chi-restraints excluded: chain S residue 228 GLU Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain S residue 233 THR Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 115 GLU Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain U residue 89 ARG Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain V residue 93 GLU Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 282 GLU Chi-restraints excluded: chain W residue 179 VAL Chi-restraints excluded: chain W residue 247 THR Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 192 ARG Chi-restraints excluded: chain X residue 195 MET Chi-restraints excluded: chain Y residue 28 LYS Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Z residue 134 GLN Chi-restraints excluded: chain Z residue 139 GLN Chi-restraints excluded: chain Z residue 141 VAL Chi-restraints excluded: chain Z residue 251 GLN Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 226 VAL Chi-restraints excluded: chain a residue 234 ASP Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain b residue 189 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 406 optimal weight: 9.9990 chunk 528 optimal weight: 8.9990 chunk 374 optimal weight: 9.9990 chunk 276 optimal weight: 2.9990 chunk 410 optimal weight: 5.9990 chunk 384 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 605 optimal weight: 4.9990 chunk 76 optimal weight: 0.0570 chunk 338 optimal weight: 2.9990 chunk 512 optimal weight: 7.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 143 ASN B 61 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN G 62 ASN G 178 ASN G 196 HIS G 219 ASN H 147 ASN K 73 HIS L 139 GLN L 302 GLN N 111 HIS O 93 GLN O 143 ASN P 61 GLN Q 94 ASN S 149 ASN U 62 ASN U 178 ASN U 196 HIS U 219 ASN V 147 ASN Y 73 HIS Z 139 GLN Z 180 ASN Z 302 GLN b 111 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121034 restraints weight = 51679.669| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.10 r_work: 0.3284 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 49400 Z= 0.279 Angle : 0.641 8.433 66842 Z= 0.348 Chirality : 0.046 0.169 7506 Planarity : 0.005 0.063 8636 Dihedral : 6.195 66.788 6902 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.97 % Rotamer: Outliers : 3.75 % Allowed : 15.26 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.10), residues: 6194 helix: 1.80 (0.10), residues: 2344 sheet: 0.60 (0.13), residues: 1478 loop : -0.45 (0.12), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Z 165 HIS 0.008 0.001 HIS P 187 PHE 0.021 0.002 PHE a 177 TYR 0.021 0.002 TYR T 117 ARG 0.009 0.001 ARG M 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 690 time to evaluate : 4.282 Fit side-chains REVERT: A 173 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7310 (mttp) REVERT: A 241 GLU cc_start: 0.6594 (pt0) cc_final: 0.6107 (pt0) REVERT: B 183 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5875 (tt0) REVERT: B 225 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7199 (ttpt) REVERT: C 8 ARG cc_start: 0.6250 (mtt-85) cc_final: 0.5931 (mtp85) REVERT: C 115 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: C 118 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7377 (mtm110) REVERT: C 142 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8363 (mm) REVERT: C 178 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6762 (tt0) REVERT: C 184 ASP cc_start: 0.6924 (m-30) cc_final: 0.6577 (t70) REVERT: D 15 HIS cc_start: 0.6229 (m170) cc_final: 0.5960 (m90) REVERT: D 24 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7530 (mm-30) REVERT: D 141 GLN cc_start: 0.6619 (tt0) cc_final: 0.6097 (tp-100) REVERT: D 143 HIS cc_start: 0.8096 (m170) cc_final: 0.7738 (m170) REVERT: D 206 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7547 (tt) REVERT: D 217 MET cc_start: 0.5827 (ttp) cc_final: 0.5497 (ttp) REVERT: E 10 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5492 (mtp180) REVERT: E 66 LYS cc_start: 0.7711 (mttp) cc_final: 0.7437 (mmtm) REVERT: E 119 LEU cc_start: 0.7713 (tp) cc_final: 0.7442 (tp) REVERT: E 122 ARG cc_start: 0.6621 (mtt180) cc_final: 0.6196 (mtp180) REVERT: E 132 LEU cc_start: 0.5320 (OUTLIER) cc_final: 0.4624 (mp) REVERT: E 152 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7830 (mt0) REVERT: E 216 GLU cc_start: 0.6363 (mt-10) cc_final: 0.5688 (tp30) REVERT: F 167 GLN cc_start: 0.7611 (tp40) cc_final: 0.7209 (tp-100) REVERT: F 174 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6767 (mt-10) REVERT: G 200 ASP cc_start: 0.5797 (t0) cc_final: 0.5562 (t0) REVERT: H 63 LYS cc_start: 0.7930 (tppt) cc_final: 0.7668 (mmtp) REVERT: H 93 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: H 282 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5993 (pt0) REVERT: I 98 LYS cc_start: 0.8028 (mppt) cc_final: 0.7443 (mmpt) REVERT: I 248 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7397 (ptmm) REVERT: J 68 ARG cc_start: 0.8233 (mtt-85) cc_final: 0.7909 (mmt180) REVERT: J 134 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7097 (pm20) REVERT: J 192 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7000 (mtt-85) REVERT: K 1 MET cc_start: 0.5143 (ttm) cc_final: 0.4792 (mmm) REVERT: K 28 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8002 (mtmm) REVERT: K 50 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7430 (mp0) REVERT: K 98 ASP cc_start: 0.7131 (m-30) cc_final: 0.6789 (p0) REVERT: K 116 SER cc_start: 0.6401 (p) cc_final: 0.6136 (m) REVERT: K 200 GLU cc_start: 0.7566 (pt0) cc_final: 0.7211 (pt0) REVERT: L 134 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6307 (tm-30) REVERT: L 163 GLN cc_start: 0.8168 (mt0) cc_final: 0.7953 (mt0) REVERT: L 251 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7515 (tp40) REVERT: N 72 MET cc_start: 0.8050 (mtp) cc_final: 0.7760 (mtm) REVERT: N 212 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: O 173 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7331 (mttp) REVERT: P 225 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7202 (ttpt) REVERT: Q 8 ARG cc_start: 0.6260 (mtt-85) cc_final: 0.5942 (mtp85) REVERT: Q 90 TYR cc_start: 0.7978 (m-10) cc_final: 0.7693 (m-80) REVERT: Q 115 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: Q 118 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7394 (mtm110) REVERT: Q 142 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8363 (mm) REVERT: Q 178 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6765 (tt0) REVERT: Q 184 ASP cc_start: 0.6927 (m-30) cc_final: 0.6576 (t70) REVERT: R 15 HIS cc_start: 0.6233 (m170) cc_final: 0.5967 (m90) REVERT: R 24 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7536 (mm-30) REVERT: R 141 GLN cc_start: 0.6603 (tt0) cc_final: 0.6077 (tp-100) REVERT: R 143 HIS cc_start: 0.8094 (m170) cc_final: 0.7744 (m170) REVERT: R 206 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7543 (tt) REVERT: R 217 MET cc_start: 0.5845 (ttp) cc_final: 0.5518 (ttp) REVERT: S 10 ARG cc_start: 0.6062 (OUTLIER) cc_final: 0.5522 (mtp180) REVERT: S 66 LYS cc_start: 0.7698 (mttp) cc_final: 0.7416 (mmtm) REVERT: S 119 LEU cc_start: 0.7717 (tp) cc_final: 0.7448 (tp) REVERT: S 122 ARG cc_start: 0.6588 (mtt180) cc_final: 0.6168 (mtp180) REVERT: S 132 LEU cc_start: 0.5345 (OUTLIER) cc_final: 0.4645 (mp) REVERT: S 152 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7845 (mt0) REVERT: S 216 GLU cc_start: 0.6358 (mt-10) cc_final: 0.5680 (tp30) REVERT: T 167 GLN cc_start: 0.7611 (tp40) cc_final: 0.7206 (tp-100) REVERT: T 174 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6751 (mt-10) REVERT: T 231 ARG cc_start: 0.6308 (OUTLIER) cc_final: 0.5314 (tpm-80) REVERT: U 89 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7762 (tpt-90) REVERT: U 200 ASP cc_start: 0.5798 (t0) cc_final: 0.5580 (t0) REVERT: V 63 LYS cc_start: 0.7932 (tppt) cc_final: 0.7672 (mmtp) REVERT: V 93 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7361 (tm-30) REVERT: V 282 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6010 (pt0) REVERT: W 98 LYS cc_start: 0.8029 (mppt) cc_final: 0.7443 (mmpt) REVERT: W 248 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7401 (ptmm) REVERT: X 68 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7910 (mmt180) REVERT: X 134 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: X 192 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6994 (mtt-85) REVERT: Y 1 MET cc_start: 0.5126 (ttm) cc_final: 0.4801 (mmm) REVERT: Y 28 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.7999 (mtmm) REVERT: Y 50 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7432 (mp0) REVERT: Y 98 ASP cc_start: 0.7132 (m-30) cc_final: 0.6799 (p0) REVERT: Y 116 SER cc_start: 0.6398 (p) cc_final: 0.6044 (m) REVERT: Y 117 ASP cc_start: 0.6392 (OUTLIER) cc_final: 0.6171 (t0) REVERT: Y 200 GLU cc_start: 0.7553 (pt0) cc_final: 0.7207 (pt0) REVERT: Z 134 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6311 (tm-30) REVERT: Z 163 GLN cc_start: 0.8185 (mt0) cc_final: 0.7970 (mt0) REVERT: Z 251 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7518 (tp40) REVERT: b 212 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6669 (mp0) outliers start: 194 outliers final: 94 residues processed: 816 average time/residue: 1.5412 time to fit residues: 1522.3292 Evaluate side-chains 826 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 688 time to evaluate : 4.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 248 LYS Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 192 ARG Chi-restraints excluded: chain J residue 195 MET Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 139 GLN Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 251 GLN Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 234 ASP Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain N residue 189 SER Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 173 LYS Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 225 LYS Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 115 ASP Chi-restraints excluded: chain Q residue 118 ARG Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 178 GLN Chi-restraints excluded: chain Q residue 192 ASP Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain S residue 10 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 152 GLN Chi-restraints excluded: chain S residue 228 GLU Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain S residue 233 THR Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 115 GLU Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 231 ARG Chi-restraints excluded: chain U residue 89 ARG Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain U residue 202 SER Chi-restraints excluded: chain V residue 93 GLU Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 282 GLU Chi-restraints excluded: chain W residue 247 THR Chi-restraints excluded: chain W residue 248 LYS Chi-restraints excluded: chain W residue 268 ILE Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 192 ARG Chi-restraints excluded: chain X residue 195 MET Chi-restraints excluded: chain Y residue 28 LYS Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Y residue 117 ASP Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Z residue 134 GLN Chi-restraints excluded: chain Z residue 139 GLN Chi-restraints excluded: chain Z residue 141 VAL Chi-restraints excluded: chain Z residue 251 GLN Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 226 VAL Chi-restraints excluded: chain a residue 234 ASP Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain b residue 189 SER Chi-restraints excluded: chain b residue 212 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 539 optimal weight: 5.9990 chunk 476 optimal weight: 3.9990 chunk 609 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 445 optimal weight: 0.7980 chunk 341 optimal weight: 6.9990 chunk 458 optimal weight: 0.4980 chunk 362 optimal weight: 0.7980 chunk 280 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 390 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 143 ASN B 61 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN G 31 ASN G 62 ASN G 178 ASN G 196 HIS G 219 ASN H 147 ASN K 73 HIS L 139 GLN L 180 ASN L 302 GLN O 93 GLN O 143 ASN P 61 GLN P 187 HIS Q 94 ASN ** Q 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 ASN U 31 ASN U 62 ASN U 178 ASN U 196 HIS U 219 ASN V 147 ASN Y 73 HIS Z 139 GLN Z 180 ASN Z 302 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.144553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122980 restraints weight = 51697.720| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.04 r_work: 0.3316 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 49400 Z= 0.186 Angle : 0.564 8.131 66842 Z= 0.307 Chirality : 0.044 0.171 7506 Planarity : 0.004 0.052 8636 Dihedral : 5.925 69.415 6902 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 2.82 % Allowed : 16.25 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.10), residues: 6194 helix: 2.07 (0.11), residues: 2352 sheet: 0.60 (0.13), residues: 1464 loop : -0.35 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Z 165 HIS 0.006 0.001 HIS U 196 PHE 0.019 0.002 PHE a 177 TYR 0.017 0.001 TYR M 130 ARG 0.010 0.000 ARG I 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 718 time to evaluate : 4.227 Fit side-chains REVERT: A 196 LYS cc_start: 0.8122 (tttt) cc_final: 0.7730 (ttmt) REVERT: A 241 GLU cc_start: 0.6574 (pt0) cc_final: 0.6103 (pt0) REVERT: C 8 ARG cc_start: 0.6249 (mtt-85) cc_final: 0.5939 (mtp85) REVERT: C 115 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: C 118 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7321 (mtm110) REVERT: C 142 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8349 (mm) REVERT: C 165 TRP cc_start: 0.8315 (m100) cc_final: 0.8040 (m100) REVERT: C 178 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6783 (tt0) REVERT: C 184 ASP cc_start: 0.6863 (m-30) cc_final: 0.6505 (t70) REVERT: C 234 GLU cc_start: 0.6963 (mp0) cc_final: 0.6685 (mm-30) REVERT: D 4 ASP cc_start: 0.6794 (OUTLIER) cc_final: 0.6527 (t0) REVERT: D 15 HIS cc_start: 0.6292 (m170) cc_final: 0.6026 (m-70) REVERT: D 24 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7501 (mm-30) REVERT: D 61 LYS cc_start: 0.7050 (mmtp) cc_final: 0.6411 (mptt) REVERT: D 141 GLN cc_start: 0.6606 (tt0) cc_final: 0.6129 (tp40) REVERT: D 143 HIS cc_start: 0.8030 (m170) cc_final: 0.7642 (OUTLIER) REVERT: D 206 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7554 (tt) REVERT: D 217 MET cc_start: 0.5837 (ttp) cc_final: 0.5550 (ttp) REVERT: E 10 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.5486 (mtp180) REVERT: E 66 LYS cc_start: 0.7733 (mttp) cc_final: 0.7465 (mmtm) REVERT: E 119 LEU cc_start: 0.7681 (tp) cc_final: 0.7422 (tp) REVERT: E 122 ARG cc_start: 0.6576 (mtt180) cc_final: 0.6178 (mtp180) REVERT: E 132 LEU cc_start: 0.5356 (OUTLIER) cc_final: 0.4649 (mp) REVERT: E 152 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7813 (mt0) REVERT: E 216 GLU cc_start: 0.6303 (mt-10) cc_final: 0.5626 (tp30) REVERT: F 127 ARG cc_start: 0.7381 (ttp-110) cc_final: 0.6602 (ttp80) REVERT: F 167 GLN cc_start: 0.7584 (tp40) cc_final: 0.7278 (tp-100) REVERT: F 174 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6646 (mt-10) REVERT: G 200 ASP cc_start: 0.5768 (t0) cc_final: 0.5536 (t0) REVERT: H 63 LYS cc_start: 0.7875 (tppt) cc_final: 0.7644 (mmtp) REVERT: H 93 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: I 98 LYS cc_start: 0.7998 (mppt) cc_final: 0.7437 (mmpt) REVERT: I 248 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7397 (ptmm) REVERT: J 68 ARG cc_start: 0.8220 (mtt-85) cc_final: 0.7888 (mmt180) REVERT: J 134 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6980 (pm20) REVERT: J 192 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6952 (mtt-85) REVERT: K 1 MET cc_start: 0.4862 (ttm) cc_final: 0.4627 (mmm) REVERT: K 28 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7969 (mtmm) REVERT: K 50 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7400 (mp0) REVERT: K 116 SER cc_start: 0.6428 (p) cc_final: 0.6170 (m) REVERT: K 200 GLU cc_start: 0.7542 (pt0) cc_final: 0.7203 (pt0) REVERT: L 134 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6234 (tm-30) REVERT: L 163 GLN cc_start: 0.8141 (mt0) cc_final: 0.7941 (mt0) REVERT: L 251 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7484 (tp40) REVERT: N 72 MET cc_start: 0.7996 (mtp) cc_final: 0.7621 (mtm) REVERT: N 212 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: O 196 LYS cc_start: 0.8153 (tttt) cc_final: 0.7714 (ttmt) REVERT: O 241 GLU cc_start: 0.6559 (pt0) cc_final: 0.6088 (pt0) REVERT: Q 8 ARG cc_start: 0.6256 (mtt-85) cc_final: 0.5944 (mtp85) REVERT: Q 90 TYR cc_start: 0.7946 (m-10) cc_final: 0.7675 (m-80) REVERT: Q 115 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: Q 118 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7341 (mtm110) REVERT: Q 142 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8349 (mm) REVERT: Q 165 TRP cc_start: 0.8319 (m100) cc_final: 0.8035 (m100) REVERT: Q 178 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6777 (tt0) REVERT: Q 184 ASP cc_start: 0.6862 (m-30) cc_final: 0.6504 (t70) REVERT: R 4 ASP cc_start: 0.6795 (OUTLIER) cc_final: 0.6541 (t0) REVERT: R 15 HIS cc_start: 0.6280 (m170) cc_final: 0.6008 (m90) REVERT: R 24 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7509 (mm-30) REVERT: R 61 LYS cc_start: 0.7057 (mmtp) cc_final: 0.6416 (mptt) REVERT: R 141 GLN cc_start: 0.6586 (tt0) cc_final: 0.6107 (tp40) REVERT: R 143 HIS cc_start: 0.8041 (m170) cc_final: 0.7655 (OUTLIER) REVERT: R 206 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7553 (tt) REVERT: R 217 MET cc_start: 0.5853 (ttp) cc_final: 0.5570 (ttp) REVERT: S 10 ARG cc_start: 0.6039 (OUTLIER) cc_final: 0.5511 (mtp180) REVERT: S 66 LYS cc_start: 0.7730 (mttp) cc_final: 0.7460 (mmtm) REVERT: S 119 LEU cc_start: 0.7684 (tp) cc_final: 0.7422 (tp) REVERT: S 122 ARG cc_start: 0.6583 (mtt180) cc_final: 0.6186 (mtp180) REVERT: S 132 LEU cc_start: 0.5365 (OUTLIER) cc_final: 0.4642 (mp) REVERT: S 152 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7821 (mt0) REVERT: S 216 GLU cc_start: 0.6307 (mt-10) cc_final: 0.5635 (tp30) REVERT: T 167 GLN cc_start: 0.7581 (tp40) cc_final: 0.7275 (tp-100) REVERT: T 174 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6658 (mt-10) REVERT: T 231 ARG cc_start: 0.6281 (mmm160) cc_final: 0.5337 (tpm-80) REVERT: U 89 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7624 (tpt170) REVERT: U 200 ASP cc_start: 0.5777 (t0) cc_final: 0.5563 (t0) REVERT: V 63 LYS cc_start: 0.7872 (tppt) cc_final: 0.7644 (mmtp) REVERT: V 93 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: V 282 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6266 (pt0) REVERT: W 98 LYS cc_start: 0.8001 (mppt) cc_final: 0.7430 (mmpt) REVERT: W 248 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7403 (ptmm) REVERT: X 68 ARG cc_start: 0.8212 (mtt-85) cc_final: 0.7878 (mmt180) REVERT: X 134 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6993 (pm20) REVERT: X 192 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6945 (mtt-85) REVERT: Y 1 MET cc_start: 0.4880 (ttm) cc_final: 0.4644 (mmm) REVERT: Y 28 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7957 (mtmm) REVERT: Y 50 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7402 (mp0) REVERT: Y 116 SER cc_start: 0.6409 (p) cc_final: 0.6091 (m) REVERT: Y 200 GLU cc_start: 0.7554 (pt0) cc_final: 0.7217 (pt0) REVERT: Z 134 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6235 (tm-30) REVERT: Z 163 GLN cc_start: 0.8158 (mt0) cc_final: 0.7952 (mt0) REVERT: Z 251 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7483 (tp40) REVERT: b 72 MET cc_start: 0.7991 (mtp) cc_final: 0.7649 (mtm) REVERT: b 212 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6723 (mp0) outliers start: 146 outliers final: 80 residues processed: 811 average time/residue: 1.5313 time to fit residues: 1508.1375 Evaluate side-chains 803 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 687 time to evaluate : 4.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 248 LYS Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 192 ARG Chi-restraints excluded: chain J residue 195 MET Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 139 GLN Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 251 GLN Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain N residue 189 SER Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 115 ASP Chi-restraints excluded: chain Q residue 118 ARG Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 178 GLN Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain S residue 10 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 152 GLN Chi-restraints excluded: chain S residue 228 GLU Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain S residue 233 THR Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 111 GLU Chi-restraints excluded: chain T residue 115 GLU Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain U residue 89 ARG Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain U residue 202 SER Chi-restraints excluded: chain V residue 93 GLU Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 282 GLU Chi-restraints excluded: chain W residue 248 LYS Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 192 ARG Chi-restraints excluded: chain X residue 195 MET Chi-restraints excluded: chain Y residue 28 LYS Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Z residue 134 GLN Chi-restraints excluded: chain Z residue 139 GLN Chi-restraints excluded: chain Z residue 141 VAL Chi-restraints excluded: chain Z residue 251 GLN Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 226 VAL Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain b residue 189 SER Chi-restraints excluded: chain b residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 512 optimal weight: 5.9990 chunk 315 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 111 optimal weight: 0.0870 chunk 543 optimal weight: 10.0000 chunk 138 optimal weight: 0.6980 chunk 436 optimal weight: 6.9990 chunk 528 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 529 optimal weight: 5.9990 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 143 ASN B 61 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN E 149 ASN G 31 ASN G 62 ASN G 178 ASN G 196 HIS G 219 ASN H 147 ASN K 73 HIS L 139 GLN L 302 GLN O 93 GLN O 143 ASN P 61 GLN Q 94 ASN ** Q 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 ASN U 31 ASN U 62 ASN U 178 ASN U 196 HIS U 219 ASN V 147 ASN Y 73 HIS Z 139 GLN Z 302 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.143450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121673 restraints weight = 51676.971| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.10 r_work: 0.3293 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 49400 Z= 0.248 Angle : 0.620 8.229 66842 Z= 0.336 Chirality : 0.045 0.177 7506 Planarity : 0.005 0.055 8636 Dihedral : 6.091 67.430 6902 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.11 % Favored : 97.85 % Rotamer: Outliers : 2.86 % Allowed : 16.52 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.10), residues: 6194 helix: 1.92 (0.10), residues: 2350 sheet: 0.60 (0.13), residues: 1478 loop : -0.39 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Z 165 HIS 0.007 0.001 HIS G 196 PHE 0.021 0.002 PHE a 177 TYR 0.019 0.002 TYR F 117 ARG 0.011 0.001 ARG W 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12388 Ramachandran restraints generated. 6194 Oldfield, 0 Emsley, 6194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 691 time to evaluate : 4.235 Fit side-chains REVERT: A 241 GLU cc_start: 0.6567 (pt0) cc_final: 0.6076 (pt0) REVERT: C 8 ARG cc_start: 0.6299 (mtt-85) cc_final: 0.5932 (mtp85) REVERT: C 115 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7684 (m-30) REVERT: C 118 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7321 (mtm110) REVERT: C 142 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8355 (mm) REVERT: C 178 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6777 (tt0) REVERT: C 184 ASP cc_start: 0.6856 (m-30) cc_final: 0.6510 (t70) REVERT: D 15 HIS cc_start: 0.6222 (m170) cc_final: 0.5964 (m-70) REVERT: D 24 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7524 (mm-30) REVERT: D 61 LYS cc_start: 0.7078 (mmtp) cc_final: 0.6422 (mptt) REVERT: D 141 GLN cc_start: 0.6630 (tt0) cc_final: 0.6107 (tp40) REVERT: D 143 HIS cc_start: 0.8089 (m170) cc_final: 0.7741 (m170) REVERT: D 206 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7517 (tt) REVERT: D 217 MET cc_start: 0.5844 (ttp) cc_final: 0.5535 (ttp) REVERT: D 230 GLU cc_start: 0.5228 (tp30) cc_final: 0.4607 (tt0) REVERT: E 10 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.5480 (mtp180) REVERT: E 66 LYS cc_start: 0.7721 (mttp) cc_final: 0.7449 (mmtm) REVERT: E 119 LEU cc_start: 0.7717 (tp) cc_final: 0.7447 (tp) REVERT: E 122 ARG cc_start: 0.6581 (mtt180) cc_final: 0.6178 (mtp180) REVERT: E 132 LEU cc_start: 0.5329 (OUTLIER) cc_final: 0.4635 (mp) REVERT: E 152 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: E 216 GLU cc_start: 0.6362 (mt-10) cc_final: 0.5682 (tp30) REVERT: F 127 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.6652 (ttp80) REVERT: F 167 GLN cc_start: 0.7605 (tp40) cc_final: 0.7200 (tp-100) REVERT: F 174 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6725 (mt-10) REVERT: G 200 ASP cc_start: 0.5740 (t0) cc_final: 0.5519 (t0) REVERT: H 63 LYS cc_start: 0.7926 (tppt) cc_final: 0.7667 (mmtp) REVERT: H 93 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: H 282 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6276 (pt0) REVERT: I 98 LYS cc_start: 0.8013 (mppt) cc_final: 0.7420 (mmpt) REVERT: I 248 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7401 (ptmm) REVERT: J 68 ARG cc_start: 0.8244 (mtt-85) cc_final: 0.7918 (mmt180) REVERT: J 134 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7052 (pm20) REVERT: J 192 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.6987 (mtt-85) REVERT: K 1 MET cc_start: 0.4901 (ttm) cc_final: 0.4661 (mmm) REVERT: K 28 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7969 (mtmm) REVERT: K 50 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7413 (mp0) REVERT: K 116 SER cc_start: 0.6449 (p) cc_final: 0.6201 (m) REVERT: K 200 GLU cc_start: 0.7587 (pt0) cc_final: 0.7236 (pt0) REVERT: L 134 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6281 (tm-30) REVERT: L 163 GLN cc_start: 0.8163 (mt0) cc_final: 0.7947 (mt0) REVERT: L 251 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7528 (tp40) REVERT: N 72 MET cc_start: 0.8062 (mtp) cc_final: 0.7762 (mtm) REVERT: N 212 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: O 241 GLU cc_start: 0.6573 (pt0) cc_final: 0.6080 (pt0) REVERT: Q 8 ARG cc_start: 0.6284 (mtt-85) cc_final: 0.5939 (mtp85) REVERT: Q 90 TYR cc_start: 0.7960 (m-10) cc_final: 0.7689 (m-80) REVERT: Q 115 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: Q 118 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7336 (mtm110) REVERT: Q 142 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8354 (mm) REVERT: Q 178 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6774 (tt0) REVERT: Q 184 ASP cc_start: 0.6857 (m-30) cc_final: 0.6541 (t70) REVERT: Q 234 GLU cc_start: 0.6991 (mp0) cc_final: 0.6699 (mm-30) REVERT: R 15 HIS cc_start: 0.6223 (m170) cc_final: 0.5962 (m90) REVERT: R 24 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7532 (mm-30) REVERT: R 61 LYS cc_start: 0.7080 (mmtp) cc_final: 0.6428 (mptt) REVERT: R 141 GLN cc_start: 0.6611 (tt0) cc_final: 0.6090 (tp40) REVERT: R 143 HIS cc_start: 0.8086 (m170) cc_final: 0.7740 (m170) REVERT: R 206 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7520 (tt) REVERT: R 217 MET cc_start: 0.5844 (ttp) cc_final: 0.5539 (ttp) REVERT: R 230 GLU cc_start: 0.5226 (tp30) cc_final: 0.4602 (tt0) REVERT: S 10 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.5483 (mtp180) REVERT: S 66 LYS cc_start: 0.7729 (mttp) cc_final: 0.7455 (mmtm) REVERT: S 119 LEU cc_start: 0.7716 (tp) cc_final: 0.7441 (tp) REVERT: S 122 ARG cc_start: 0.6561 (mtt180) cc_final: 0.6166 (mtp180) REVERT: S 132 LEU cc_start: 0.5387 (OUTLIER) cc_final: 0.4679 (mp) REVERT: S 152 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7812 (mt0) REVERT: S 216 GLU cc_start: 0.6354 (mt-10) cc_final: 0.5677 (tp30) REVERT: T 167 GLN cc_start: 0.7605 (tp40) cc_final: 0.7196 (tp-100) REVERT: T 174 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6726 (mt-10) REVERT: T 231 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.5326 (tpm-80) REVERT: U 200 ASP cc_start: 0.5801 (t0) cc_final: 0.5585 (t0) REVERT: V 63 LYS cc_start: 0.7926 (tppt) cc_final: 0.7665 (mmtp) REVERT: V 93 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: V 282 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6286 (pt0) REVERT: W 98 LYS cc_start: 0.8015 (mppt) cc_final: 0.7423 (mmpt) REVERT: W 248 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7407 (ptmm) REVERT: X 68 ARG cc_start: 0.8238 (mtt-85) cc_final: 0.7914 (mmt180) REVERT: X 134 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7053 (pm20) REVERT: X 192 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6972 (mtt-85) REVERT: Y 1 MET cc_start: 0.4926 (ttm) cc_final: 0.4671 (mmm) REVERT: Y 28 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7962 (mtmm) REVERT: Y 50 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7410 (mp0) REVERT: Y 116 SER cc_start: 0.6406 (p) cc_final: 0.6137 (m) REVERT: Y 117 ASP cc_start: 0.6383 (OUTLIER) cc_final: 0.6162 (t0) REVERT: Y 200 GLU cc_start: 0.7583 (pt0) cc_final: 0.7238 (pt0) REVERT: Z 134 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6289 (tm-30) REVERT: Z 163 GLN cc_start: 0.8176 (mt0) cc_final: 0.7959 (mt0) REVERT: Z 251 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7525 (tp40) REVERT: b 72 MET cc_start: 0.8057 (mtp) cc_final: 0.7724 (mtm) REVERT: b 212 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6708 (mp0) outliers start: 148 outliers final: 83 residues processed: 784 average time/residue: 1.5511 time to fit residues: 1471.6242 Evaluate side-chains 799 residues out of total 5170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 678 time to evaluate : 4.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain I residue 248 LYS Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 192 ARG Chi-restraints excluded: chain J residue 195 MET Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 251 GLN Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 189 SER Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 231 ILE Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 115 ASP Chi-restraints excluded: chain Q residue 118 ARG Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 178 GLN Chi-restraints excluded: chain Q residue 192 ASP Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain S residue 10 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 152 GLN Chi-restraints excluded: chain S residue 228 GLU Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain S residue 233 THR Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 111 GLU Chi-restraints excluded: chain T residue 115 GLU Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 231 ARG Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain U residue 202 SER Chi-restraints excluded: chain V residue 93 GLU Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 282 GLU Chi-restraints excluded: chain W residue 248 LYS Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 192 ARG Chi-restraints excluded: chain X residue 195 MET Chi-restraints excluded: chain Y residue 28 LYS Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Y residue 117 ASP Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Z residue 134 GLN Chi-restraints excluded: chain Z residue 141 VAL Chi-restraints excluded: chain Z residue 251 GLN Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 226 VAL Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain b residue 189 SER Chi-restraints excluded: chain b residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 127 optimal weight: 4.9990 chunk 267 optimal weight: 0.9990 chunk 332 optimal weight: 5.9990 chunk 467 optimal weight: 10.0000 chunk 287 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 390 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 143 ASN B 61 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN G 31 ASN G 62 ASN G 178 ASN G 219 ASN H 147 ASN K 73 HIS L 139 GLN L 180 ASN L 302 GLN O 93 GLN O 143 ASN P 61 GLN ** P 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN ** Q 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 ASN U 31 ASN U 62 ASN U 178 ASN U 219 ASN V 147 ASN Y 73 HIS Z 139 GLN Z 180 ASN Z 302 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.143172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.121402 restraints weight = 51558.777| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.12 r_work: 0.3288 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 49400 Z= 0.265 Angle : 0.639 8.408 66842 Z= 0.346 Chirality : 0.046 0.177 7506 Planarity : 0.005 0.058 8636 Dihedral : 6.163 66.905 6902 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.13 % Favored : 97.84 % Rotamer: Outliers : 2.92 % Allowed : 16.50 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.10), residues: 6194 helix: 1.85 (0.10), residues: 2346 sheet: 0.58 (0.13), residues: 1482 loop : -0.45 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 165 HIS 0.007 0.001 HIS G 196 PHE 0.021 0.002 PHE a 177 TYR 0.020 0.002 TYR T 117 ARG 0.010 0.001 ARG W 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38056.19 seconds wall clock time: 649 minutes 13.30 seconds (38953.30 seconds total)