Starting phenix.real_space_refine on Tue Sep 24 04:13:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm7_4590/09_2024/6qm7_4590.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm7_4590/09_2024/6qm7_4590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm7_4590/09_2024/6qm7_4590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm7_4590/09_2024/6qm7_4590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm7_4590/09_2024/6qm7_4590.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm7_4590/09_2024/6qm7_4590.cif" } resolution = 2.8 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= 0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians S 328 5.16 5 C 30912 2.51 5 N 8480 2.21 5 O 9796 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 512 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 49518 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1857 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "B" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "C" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2195 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "D" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1873 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 4, 'TRANS': 234} Chain: "E" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1756 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "F" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "G" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1727 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1710 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "I" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "J" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "K" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "L" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1579 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 2, 'TRANS': 199} Chain: "M" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "N" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "O" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1857 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "P" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "Q" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2195 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "R" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1873 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 4, 'TRANS': 234} Chain: "S" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1756 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "T" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "U" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1727 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "V" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1710 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "W" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "X" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "Y" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "Z" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1579 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 2, 'TRANS': 199} Chain: "a" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "b" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'J6E': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'J6E': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "I" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "K" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "M" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "N" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "O" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "P" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "Q" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "S" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "T" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "U" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "V" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "W" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "X" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "Y" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Z" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "a" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "b" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 19.52, per 1000 atoms: 0.39 Number of scatterers: 49518 At special positions: 0 Unit cell: (151.94, 203.3, 138.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 328 16.00 F 2 9.00 O 9796 8.00 N 8480 7.00 C 30912 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: 8.49 Conformation dependent library (CDL) restraints added in 4.6 seconds 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11708 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 70 sheets defined 39.2% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.29 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.626A pdb=" N LYS A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 30 " --> pdb=" O PHE A 26 " (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: 3.609A pdb=" N ARG A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 188 removed outlier: 3.627A pdb=" N LYS A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 235 through 249 removed outlier: 3.554A pdb=" N ALA A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 29 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 77 through 100 removed outlier: 3.639A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 122 removed outlier: 3.560A pdb=" N ILE B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 176 Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.767A pdb=" N GLY B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.552A pdb=" N TYR B 227 " --> pdb=" O GLN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 85 through 108 Processing helix chain 'C' and resid 112 through 127 removed outlier: 3.935A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 185 removed outlier: 3.798A pdb=" N ASP C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 Processing helix chain 'C' and resid 230 through 234 Processing helix chain 'C' and resid 250 through 277 Proline residue: C 256 - end of helix removed outlier: 3.638A pdb=" N GLN C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 29 Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 103 through 119 removed outlier: 3.524A pdb=" N THR D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 removed outlier: 3.761A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER D 175 " --> pdb=" O TYR D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 218 through 240 removed outlier: 3.595A pdb=" N LYS D 224 " --> pdb=" O GLU D 220 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'E' and resid 160 through 164 Processing helix chain 'E' and resid 181 through 204 removed outlier: 3.720A pdb=" N ILE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 222 removed outlier: 3.774A pdb=" N LEU E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER E 220 " --> pdb=" O THR E 216 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN E 222 " --> pdb=" O ASP E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 285 removed outlier: 3.599A pdb=" N SER E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 306 Processing helix chain 'E' and resid 331 through 341 removed outlier: 3.508A pdb=" N ILE E 338 " --> pdb=" O GLU E 334 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG E 341 " --> pdb=" O ALA E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.672A pdb=" N VAL F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 265 Processing helix chain 'F' and resid 269 through 285 removed outlier: 3.806A pdb=" N HIS F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 341 removed outlier: 3.848A pdb=" N SER F 333 " --> pdb=" O ARG F 329 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS F 340 " --> pdb=" O TYR F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 344 No H-bonds generated for 'chain 'F' and resid 342 through 344' Processing helix chain 'F' and resid 348 through 363 removed outlier: 3.746A pdb=" N ALA F 363 " --> pdb=" O ALA F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 399 Processing helix chain 'G' and resid 6 through 10 removed outlier: 4.067A pdb=" N ASP G 9 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN G 10 " --> pdb=" O GLY G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 6 through 10' Processing helix chain 'G' and resid 21 through 33 removed outlier: 3.586A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 123 removed outlier: 3.615A pdb=" N TYR G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 Processing helix chain 'G' and resid 185 through 201 removed outlier: 3.858A pdb=" N GLY G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 125 Processing helix chain 'H' and resid 129 through 144 Processing helix chain 'H' and resid 185 through 197 removed outlier: 3.820A pdb=" N LEU H 189 " --> pdb=" O GLY H 185 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N SER H 191 " --> pdb=" O ILE H 187 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE H 192 " --> pdb=" O PHE H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 221 removed outlier: 3.788A pdb=" N ARG H 220 " --> pdb=" O HIS H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 248 Processing helix chain 'H' and resid 255 through 259 Processing helix chain 'I' and resid 77 through 100 removed outlier: 3.527A pdb=" N LEU I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 119 Processing helix chain 'I' and resid 159 through 171 Processing helix chain 'I' and resid 176 through 195 Processing helix chain 'J' and resid 56 through 78 Processing helix chain 'J' and resid 83 through 97 Processing helix chain 'J' and resid 142 through 154 removed outlier: 3.623A pdb=" N GLY J 148 " --> pdb=" O GLU J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 176 Processing helix chain 'K' and resid 50 through 72 Processing helix chain 'K' and resid 78 through 94 removed outlier: 3.524A pdb=" N ILE K 94 " --> pdb=" O LEU K 90 " (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 147 through 170 Processing helix chain 'L' and resid 174 through 189 Processing helix chain 'L' and resid 230 through 242 removed outlier: 4.074A pdb=" N GLY L 236 " --> pdb=" O ILE L 232 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL L 237 " --> pdb=" O TYR L 233 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR L 240 " --> pdb=" O GLY L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 264 Processing helix chain 'L' and resid 291 through 299 removed outlier: 3.500A pdb=" N HIS L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 204 Processing helix chain 'M' and resid 210 through 224 Processing helix chain 'M' and resid 267 through 281 Proline residue: M 273 - end of helix Processing helix chain 'M' and resid 293 through 312 Processing helix chain 'N' and resid 53 through 74 Processing helix chain 'N' and resid 80 through 98 Processing helix chain 'N' and resid 136 through 140 Processing helix chain 'N' and resid 141 through 153 removed outlier: 4.222A pdb=" N LEU N 145 " --> pdb=" O ILE N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 177 Processing helix chain 'N' and resid 208 through 211 Processing helix chain 'N' and resid 212 through 217 Processing helix chain 'O' and resid 19 through 31 removed outlier: 3.651A pdb=" N LYS O 27 " --> pdb=" O GLU O 23 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR O 30 " --> pdb=" O PHE O 26 " (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: 3.575A pdb=" N ARG O 122 " --> pdb=" O LYS O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 188 removed outlier: 3.631A pdb=" N LYS O 186 " --> pdb=" O GLU O 182 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR O 188 " --> pdb=" O ARG O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 194 through 211 Processing helix chain 'O' and resid 235 through 249 removed outlier: 3.566A pdb=" N ALA O 249 " --> pdb=" O ALA O 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 29 Processing helix chain 'P' and resid 56 through 60 Processing helix chain 'P' and resid 77 through 100 removed outlier: 3.644A pdb=" N VAL P 83 " --> pdb=" O PRO P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 120 removed outlier: 3.590A pdb=" N ILE P 115 " --> pdb=" O LYS P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 176 Processing helix chain 'P' and resid 181 through 197 removed outlier: 3.795A pdb=" N GLY P 196 " --> pdb=" O THR P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 229 removed outlier: 3.558A pdb=" N TYR P 227 " --> pdb=" O GLN P 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 6 Processing helix chain 'Q' and resid 18 through 29 Processing helix chain 'Q' and resid 85 through 108 Processing helix chain 'Q' and resid 112 through 127 removed outlier: 3.840A pdb=" N TYR Q 127 " --> pdb=" O GLU Q 123 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 185 removed outlier: 3.801A pdb=" N ASP Q 184 " --> pdb=" O LEU Q 180 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 206 Processing helix chain 'Q' and resid 250 through 277 Proline residue: Q 256 - end of helix removed outlier: 3.656A pdb=" N GLN Q 276 " --> pdb=" O GLU Q 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 28 Processing helix chain 'R' and resid 76 through 98 Processing helix chain 'R' and resid 103 through 119 removed outlier: 3.504A pdb=" N THR R 119 " --> pdb=" O GLN R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 176 removed outlier: 3.764A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER R 175 " --> pdb=" O TYR R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 194 Processing helix chain 'R' and resid 218 through 240 removed outlier: 3.601A pdb=" N LYS R 224 " --> pdb=" O GLU R 220 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE R 225 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU R 232 " --> pdb=" O GLU R 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 134 removed outlier: 3.556A pdb=" N GLU S 129 " --> pdb=" O GLU S 125 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU S 133 " --> pdb=" O GLU S 129 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY S 134 " --> pdb=" O ALA S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 204 removed outlier: 3.718A pdb=" N ILE S 187 " --> pdb=" O ALA S 183 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 222 removed outlier: 3.783A pdb=" N LEU S 219 " --> pdb=" O ALA S 215 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER S 220 " --> pdb=" O THR S 216 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN S 222 " --> pdb=" O ASP S 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 273 through 285 removed outlier: 3.572A pdb=" N SER S 279 " --> pdb=" O GLU S 275 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL S 280 " --> pdb=" O ALA S 276 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU S 283 " --> pdb=" O SER S 279 " (cutoff:3.500A) Processing helix chain 'S' and resid 290 through 306 Processing helix chain 'S' and resid 331 through 341 removed outlier: 3.608A pdb=" N ARG S 341 " --> pdb=" O ALA S 337 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 196 removed outlier: 3.674A pdb=" N VAL T 193 " --> pdb=" O ALA T 189 " (cutoff:3.500A) Processing helix chain 'T' and resid 242 through 265 Processing helix chain 'T' and resid 269 through 285 removed outlier: 3.761A pdb=" N HIS T 284 " --> pdb=" O LYS T 280 " (cutoff:3.500A) Processing helix chain 'T' and resid 329 through 341 removed outlier: 3.839A pdb=" N SER T 333 " --> pdb=" O ARG T 329 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS T 340 " --> pdb=" O TYR T 336 " (cutoff:3.500A) Processing helix chain 'T' and resid 342 through 344 No H-bonds generated for 'chain 'T' and resid 342 through 344' Processing helix chain 'T' and resid 348 through 363 removed outlier: 3.762A pdb=" N ALA T 363 " --> pdb=" O ALA T 359 " (cutoff:3.500A) Processing helix chain 'T' and resid 394 through 399 Processing helix chain 'U' and resid 6 through 10 removed outlier: 4.084A pdb=" N ASP U 9 " --> pdb=" O SER U 6 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN U 10 " --> pdb=" O GLY U 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 6 through 10' Processing helix chain 'U' and resid 21 through 33 removed outlier: 3.587A pdb=" N VAL U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 104 Processing helix chain 'U' and resid 108 through 123 removed outlier: 3.642A pdb=" N TYR U 123 " --> pdb=" O PHE U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 177 Processing helix chain 'U' and resid 185 through 201 removed outlier: 3.838A pdb=" N GLY U 191 " --> pdb=" O ASP U 187 " (cutoff:3.500A) Processing helix chain 'V' and resid 102 through 125 Processing helix chain 'V' and resid 129 through 144 Processing helix chain 'V' and resid 185 through 197 removed outlier: 3.866A pdb=" N LEU V 189 " --> pdb=" O GLY V 185 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER V 191 " --> pdb=" O ILE V 187 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE V 192 " --> pdb=" O PHE V 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 221 removed outlier: 3.825A pdb=" N ARG V 220 " --> pdb=" O HIS V 216 " (cutoff:3.500A) Processing helix chain 'V' and resid 244 through 248 Processing helix chain 'V' and resid 255 through 259 Processing helix chain 'W' and resid 77 through 100 Processing helix chain 'W' and resid 104 through 119 Processing helix chain 'W' and resid 159 through 171 Processing helix chain 'W' and resid 176 through 195 Processing helix chain 'X' and resid 56 through 79 Processing helix chain 'X' and resid 83 through 97 Processing helix chain 'X' and resid 142 through 154 removed outlier: 3.607A pdb=" N GLY X 148 " --> pdb=" O GLU X 144 " (cutoff:3.500A) Processing helix chain 'X' and resid 159 through 176 Processing helix chain 'Y' and resid 50 through 72 Processing helix chain 'Y' and resid 78 through 95 removed outlier: 3.551A pdb=" N ILE Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) removed outlier: 4.085A 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 147 through 170 Processing helix chain 'Z' and resid 174 through 189 Processing helix chain 'Z' and resid 230 through 242 removed outlier: 4.085A pdb=" N GLY Z 236 " --> pdb=" O ILE Z 232 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL Z 237 " --> pdb=" O TYR Z 233 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR Z 240 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) Processing helix chain 'Z' and resid 247 through 266 removed outlier: 3.613A pdb=" N ARG Z 265 " --> pdb=" O HIS Z 261 " (cutoff:3.500A) Processing helix chain 'Z' and resid 291 through 299 removed outlier: 3.521A pdb=" N HIS Z 296 " --> pdb=" O THR Z 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 182 through 204 Processing helix chain 'a' and resid 210 through 224 Processing helix chain 'a' and resid 267 through 281 Proline residue: a 273 - end of helix Processing helix chain 'a' and resid 293 through 312 Processing helix chain 'b' and resid 53 through 74 Processing helix chain 'b' and resid 80 through 98 Processing helix chain 'b' and resid 136 through 140 Processing helix chain 'b' and resid 141 through 153 removed outlier: 4.232A pdb=" N LEU b 145 " --> pdb=" O ILE b 141 " (cutoff:3.500A) Processing helix chain 'b' and resid 158 through 177 Processing helix chain 'b' and resid 208 through 211 Processing helix chain 'b' and resid 212 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171 removed outlier: 5.614A 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 70 removed outlier: 6.600A pdb=" N ILE A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE A 153 " --> pdb=" O HIS A 165 " (cutoff:3.500A) 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 63 through 67 removed outlier: 6.636A 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: 6.380A pdb=" N ILE C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.030A 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 Processing sheet with id=AA8, first strand: chain 'D' and resid 63 through 64 Processing sheet with id=AA9, first strand: chain 'E' and resid 267 through 270 removed outlier: 4.719A pdb=" N VAL E 317 " --> pdb=" O TYR E 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 167 through 171 removed outlier: 6.438A pdb=" N ILE E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU E 253 " --> pdb=" O TYR E 265 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 323 through 326 removed outlier: 5.482A pdb=" N GLY F 381 " --> pdb=" O PRO F 385 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 228 through 232 removed outlier: 6.478A pdb=" N VAL F 235 " --> pdb=" O ILE F 231 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU F 309 " --> pdb=" O TYR F 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.974A pdb=" N ALA G 142 " --> pdb=" O GLY G 145 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU G 148 " --> pdb=" O TYR G 160 " (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 76 removed outlier: 6.506A pdb=" N SER H 76 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 88 through 92 removed outlier: 6.646A pdb=" N ILE H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL H 165 " --> pdb=" O LEU H 177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 153 through 157 removed outlier: 3.538A pdb=" N ASP I 219 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL I 204 " --> pdb=" O GLY I 217 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY I 217 " --> pdb=" O VAL I 204 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL I 206 " --> pdb=" O THR I 215 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR I 215 " --> pdb=" O VAL I 206 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N THR I 208 " --> pdb=" O GLU I 213 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLU I 213 " --> pdb=" O THR I 208 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 49 through 51 removed outlier: 3.556A pdb=" N ASP I 57 " --> pdb=" O ALA I 49 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU I 51 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL I 55 " --> pdb=" O GLU I 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 63 through 67 removed outlier: 6.299A pdb=" N ILE I 63 " --> pdb=" O GLY I 74 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLY I 74 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N TYR I 65 " --> pdb=" O CYS I 72 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N CYS I 72 " --> pdb=" O TYR I 65 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 240 through 247 removed outlier: 3.605A pdb=" N LYS I 242 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS J 194 " --> pdb=" O THR J 191 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N CYS J 19 " --> pdb=" O GLY J 16 " (cutoff:3.500A) removed outlier: 5.981A 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: 6.631A pdb=" N GLU J 30 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR J 34 " --> pdb=" O GLU J 30 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 42 through 46 removed outlier: 6.668A pdb=" N ILE J 49 " --> pdb=" O VAL J 45 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 140 through 143 removed outlier: 3.992A pdb=" N TYR K 13 " --> pdb=" O CYS K 10 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL K 191 " --> pdb=" O ILE K 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 22 through 24 removed outlier: 6.882A pdb=" N ASN K 22 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 36 through 40 removed outlier: 6.670A pdb=" N GLN K 43 " --> pdb=" O LEU K 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 224 through 227 removed outlier: 6.682A pdb=" N HIS L 277 " --> pdb=" O LYS L 285 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LYS L 285 " --> pdb=" O HIS L 277 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N HIS L 279 " --> pdb=" O TRP L 283 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N TRP L 283 " --> pdb=" O HIS L 279 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 119 through 121 removed outlier: 6.942A pdb=" N THR L 121 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE L 125 " --> pdb=" O THR L 121 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 133 through 135 removed outlier: 3.738A pdb=" N MET L 199 " --> pdb=" O THR L 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 261 through 265 removed outlier: 5.515A pdb=" N THR M 135 " --> pdb=" O ASP M 150 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 153 through 154 Processing sheet with id=AD5, first strand: chain 'M' and resid 168 through 172 removed outlier: 6.682A pdb=" N THR M 175 " --> pdb=" O LEU M 171 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN M 234 " --> pdb=" O TYR M 250 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER M 249 " --> pdb=" O GLU M 257 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU M 257 " --> pdb=" O SER M 249 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 29 through 32 removed outlier: 3.609A pdb=" N LEU N 29 " --> pdb=" O TYR N 26 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU N 24 " --> pdb=" O LYS N 31 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 29 through 32 removed outlier: 3.609A pdb=" N LEU N 29 " --> pdb=" O TYR N 26 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU N 24 " --> pdb=" O LYS N 31 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 132 through 135 Processing sheet with id=AD9, first strand: chain 'O' and resid 167 through 171 removed outlier: 5.568A 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 70 removed outlier: 6.581A pdb=" N ILE O 73 " --> pdb=" O VAL O 69 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE O 153 " --> pdb=" O HIS O 165 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 158 through 161 removed outlier: 3.879A pdb=" N GLY P 41 " --> pdb=" O ALA P 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 63 through 67 removed outlier: 6.643A 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: 6.406A pdb=" N ILE Q 78 " --> pdb=" O ILE Q 74 " (cutoff:3.500A) removed outlier: 4.017A 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 Processing sheet with id=AE7, first strand: chain 'R' and resid 63 through 64 Processing sheet with id=AE8, first strand: chain 'S' and resid 267 through 270 removed outlier: 4.727A pdb=" N VAL S 317 " --> pdb=" O TYR S 330 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 167 through 171 removed outlier: 6.437A pdb=" N ILE S 174 " --> pdb=" O VAL S 170 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU S 253 " --> pdb=" O TYR S 265 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 323 through 326 removed outlier: 5.497A pdb=" N GLY T 381 " --> pdb=" O PRO T 385 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 228 through 232 removed outlier: 6.496A pdb=" N VAL T 235 " --> pdb=" O ILE T 231 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU T 309 " --> pdb=" O TYR T 321 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 162 through 165 Processing sheet with id=AF4, first strand: chain 'U' and resid 67 through 69 removed outlier: 3.954A pdb=" N ALA U 142 " --> pdb=" O GLY U 145 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU U 148 " --> pdb=" O TYR U 160 " (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 76 removed outlier: 6.593A pdb=" N SER V 76 " --> pdb=" O VAL V 80 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL V 80 " --> pdb=" O SER V 76 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 88 through 92 removed outlier: 6.661A pdb=" N ILE V 95 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL V 165 " --> pdb=" O LEU V 177 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 153 through 157 removed outlier: 3.517A pdb=" N ASP W 219 " --> pdb=" O VAL W 202 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL W 204 " --> pdb=" O GLY W 217 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY W 217 " --> pdb=" O VAL W 204 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL W 206 " --> pdb=" O THR W 215 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N THR W 215 " --> pdb=" O VAL W 206 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N THR W 208 " --> pdb=" O GLU W 213 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLU W 213 " --> pdb=" O THR W 208 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 49 through 51 removed outlier: 3.572A pdb=" N ASP W 57 " --> pdb=" O ALA W 49 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU W 51 " --> pdb=" O VAL W 55 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL W 55 " --> pdb=" O GLU W 51 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 63 through 67 removed outlier: 6.354A pdb=" N ILE W 63 " --> pdb=" O GLY W 74 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLY W 74 " --> pdb=" O ILE W 63 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR W 65 " --> pdb=" O CYS W 72 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N CYS W 72 " --> pdb=" O TYR W 65 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 240 through 247 removed outlier: 3.596A pdb=" N LYS W 242 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS X 194 " --> pdb=" O THR X 191 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N CYS X 19 " --> pdb=" O GLY X 16 " (cutoff:3.500A) removed outlier: 5.958A 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: 6.841A 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 46 removed outlier: 6.662A pdb=" N ILE X 49 " --> pdb=" O VAL X 45 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Y' and resid 140 through 143 removed outlier: 4.018A pdb=" N VAL Y 191 " --> pdb=" O ILE Y 202 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 22 through 24 removed outlier: 6.863A pdb=" N ASN Y 22 " --> pdb=" O ILE Y 29 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 36 through 40 removed outlier: 6.735A pdb=" N GLN Y 43 " --> pdb=" O LEU Y 39 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 224 through 227 removed outlier: 6.651A pdb=" N HIS Z 277 " --> pdb=" O LYS Z 285 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LYS Z 285 " --> pdb=" O HIS Z 277 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N HIS Z 279 " --> pdb=" O TRP Z 283 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TRP Z 283 " --> pdb=" O HIS Z 279 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 119 through 121 removed outlier: 7.021A pdb=" N THR Z 121 " --> pdb=" O ILE Z 125 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE Z 125 " --> pdb=" O THR Z 121 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 133 through 135 removed outlier: 3.750A pdb=" N MET Z 199 " --> pdb=" O THR Z 143 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'a' and resid 261 through 265 removed outlier: 5.547A pdb=" N THR a 135 " --> pdb=" O ASP a 150 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 153 through 154 Processing sheet with id=AH4, first strand: chain 'a' and resid 168 through 172 removed outlier: 6.713A pdb=" N THR a 175 " --> pdb=" O LEU a 171 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN a 234 " --> pdb=" O TYR a 250 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER a 249 " --> pdb=" O GLU a 257 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU a 257 " --> pdb=" O SER a 249 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 29 through 32 removed outlier: 3.612A pdb=" N LEU b 29 " --> pdb=" O TYR b 26 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU b 24 " --> pdb=" O LYS b 31 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 29 through 32 removed outlier: 3.612A pdb=" N LEU b 29 " --> pdb=" O TYR b 26 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU b 24 " --> pdb=" O LYS b 31 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 132 through 135 2843 hydrogen bonds defined for protein. 8157 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: 17.54 Time building geometry restraints manager: 10.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8371 1.31 - 1.45: 13202 1.45 - 1.58: 28033 1.58 - 1.71: 0 1.71 - 1.85: 516 Bond restraints: 50122 Sorted by residual: bond pdb=" C PRO Y 53 " pdb=" O PRO Y 53 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.26e-02 6.30e+03 2.14e+01 bond pdb=" N ILE O 53 " pdb=" CA ILE O 53 " ideal model delta sigma weight residual 1.456 1.493 -0.037 8.60e-03 1.35e+04 1.88e+01 bond pdb=" N GLY D 37 " pdb=" CA GLY D 37 " ideal model delta sigma weight residual 1.442 1.475 -0.033 7.70e-03 1.69e+04 1.83e+01 bond pdb=" C PRO W 152 " pdb=" O PRO W 152 " ideal model delta sigma weight residual 1.238 1.186 0.052 1.22e-02 6.72e+03 1.83e+01 bond pdb=" C PRO K 53 " pdb=" O PRO K 53 " ideal model delta sigma weight residual 1.237 1.184 0.054 1.26e-02 6.30e+03 1.82e+01 ... (remaining 50117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 48064 2.01 - 4.02: 17560 4.02 - 6.03: 1999 6.03 - 8.04: 169 8.04 - 10.05: 18 Bond angle restraints: 67810 Sorted by residual: angle pdb=" C LEU E 138 " pdb=" N GLY E 139 " pdb=" CA GLY E 139 " ideal model delta sigma weight residual 121.65 126.78 -5.13 6.80e-01 2.16e+00 5.70e+01 angle pdb=" C THR M 232 " pdb=" CA THR M 232 " pdb=" CB THR M 232 " ideal model delta sigma weight residual 110.34 120.17 -9.83 1.40e+00 5.10e-01 4.94e+01 angle pdb=" C LEU S 138 " pdb=" N GLY S 139 " pdb=" CA GLY S 139 " ideal model delta sigma weight residual 122.18 126.74 -4.56 6.90e-01 2.10e+00 4.36e+01 angle pdb=" CA ASP N 21 " pdb=" CB ASP N 21 " pdb=" CG ASP N 21 " ideal model delta sigma weight residual 112.60 119.16 -6.56 1.00e+00 1.00e+00 4.31e+01 angle pdb=" C THR a 232 " pdb=" CA THR a 232 " pdb=" CB THR a 232 " ideal model delta sigma weight residual 110.94 118.94 -8.00 1.28e+00 6.10e-01 3.91e+01 ... (remaining 67805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 25843 18.03 - 36.05: 2922 36.05 - 54.08: 967 54.08 - 72.11: 287 72.11 - 90.14: 91 Dihedral angle restraints: 30110 sinusoidal: 11784 harmonic: 18326 Sorted by residual: dihedral pdb=" CA GLY Q 171 " pdb=" C GLY Q 171 " pdb=" N GLN Q 172 " pdb=" CA GLN Q 172 " ideal model delta harmonic sigma weight residual 180.00 -145.28 -34.72 0 5.00e+00 4.00e-02 4.82e+01 dihedral pdb=" CA GLY C 171 " pdb=" C GLY C 171 " pdb=" N GLN C 172 " pdb=" CA GLN C 172 " ideal model delta harmonic sigma weight residual -180.00 -145.84 -34.16 0 5.00e+00 4.00e-02 4.67e+01 dihedral pdb=" CA LYS J 204 " pdb=" C LYS J 204 " pdb=" N ASP J 205 " pdb=" CA ASP J 205 " ideal model delta harmonic sigma weight residual -180.00 -145.92 -34.08 0 5.00e+00 4.00e-02 4.65e+01 ... (remaining 30107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3248 0.063 - 0.126: 2872 0.126 - 0.189: 1173 0.189 - 0.252: 218 0.252 - 0.316: 33 Chirality restraints: 7544 Sorted by residual: chirality pdb=" CA ILE A 153 " pdb=" N ILE A 153 " pdb=" C ILE A 153 " pdb=" CB ILE A 153 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA THR Q 66 " pdb=" N THR Q 66 " pdb=" C THR Q 66 " pdb=" CB THR Q 66 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB THR K 82 " pdb=" CA THR K 82 " pdb=" OG1 THR K 82 " pdb=" CG2 THR K 82 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 7541 not shown) Planarity restraints: 8790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 J6E Z4000 " -0.051 2.00e-02 2.50e+03 1.14e-01 3.58e+02 pdb=" C11 J6E Z4000 " 0.120 2.00e-02 2.50e+03 pdb=" C12 J6E Z4000 " -0.068 2.00e-02 2.50e+03 pdb=" C13 J6E Z4000 " -0.123 2.00e-02 2.50e+03 pdb=" C14 J6E Z4000 " -0.082 2.00e-02 2.50e+03 pdb=" C15 J6E Z4000 " -0.121 2.00e-02 2.50e+03 pdb=" C16 J6E Z4000 " 0.028 2.00e-02 2.50e+03 pdb=" N2 J6E Z4000 " -0.059 2.00e-02 2.50e+03 pdb=" N3 J6E Z4000 " -0.038 2.00e-02 2.50e+03 pdb=" N4 J6E Z4000 " 0.164 2.00e-02 2.50e+03 pdb=" N5 J6E Z4000 " 0.229 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 J6E L4000 " -0.012 2.00e-02 2.50e+03 9.85e-02 2.67e+02 pdb=" C11 J6E L4000 " -0.098 2.00e-02 2.50e+03 pdb=" C12 J6E L4000 " 0.073 2.00e-02 2.50e+03 pdb=" C13 J6E L4000 " 0.119 2.00e-02 2.50e+03 pdb=" C14 J6E L4000 " 0.060 2.00e-02 2.50e+03 pdb=" C15 J6E L4000 " 0.076 2.00e-02 2.50e+03 pdb=" C16 J6E L4000 " 0.007 2.00e-02 2.50e+03 pdb=" N2 J6E L4000 " 0.071 2.00e-02 2.50e+03 pdb=" N3 J6E L4000 " 0.037 2.00e-02 2.50e+03 pdb=" N4 J6E L4000 " -0.114 2.00e-02 2.50e+03 pdb=" N5 J6E L4000 " -0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N J6E Z4000 " 0.105 2.00e-02 2.50e+03 1.00e-01 2.26e+02 pdb=" C J6E Z4000 " 0.064 2.00e-02 2.50e+03 pdb=" C1 J6E Z4000 " 0.067 2.00e-02 2.50e+03 pdb=" C10 J6E Z4000 " 0.024 2.00e-02 2.50e+03 pdb=" C11 J6E Z4000 " 0.117 2.00e-02 2.50e+03 pdb=" C2 J6E Z4000 " 0.013 2.00e-02 2.50e+03 pdb=" C3 J6E Z4000 " -0.096 2.00e-02 2.50e+03 pdb=" C9 J6E Z4000 " -0.193 2.00e-02 2.50e+03 pdb=" F J6E Z4000 " -0.101 2.00e-02 2.50e+03 ... (remaining 8787 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1947 2.70 - 3.25: 47003 3.25 - 3.80: 82353 3.80 - 4.35: 118177 4.35 - 4.90: 190108 Nonbonded interactions: 439588 Sorted by model distance: nonbonded pdb=" OG1 THR W 200 " pdb=" O HOH W 301 " model vdw 2.155 3.040 nonbonded pdb=" OE2 GLU E 205 " pdb=" OH TYR M 200 " model vdw 2.191 3.040 nonbonded pdb=" OE2 GLU S 205 " pdb=" OH TYR a 200 " model vdw 2.201 3.040 nonbonded pdb=" OE1 GLN A 195 " pdb=" NH1 ARG A 223 " model vdw 2.205 3.120 nonbonded pdb=" OE1 GLN O 195 " pdb=" NH1 ARG O 223 " model vdw 2.208 3.120 ... (remaining 439583 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } 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: 1.100 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: 0.040 Extract box with map and model: 1.360 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 81.540 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.300 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:8.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 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 : 0.012 0.080 50122 Z= 0.815 Angle : 1.871 10.047 67810 Z= 1.372 Chirality : 0.095 0.316 7544 Planarity : 0.006 0.114 8790 Dihedral : 18.624 90.136 18402 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.94 % Favored : 95.71 % Rotamer: Outliers : 11.11 % Allowed : 10.39 % Favored : 78.50 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.65 (0.09), residues: 6290 helix: -2.22 (0.08), residues: 2316 sheet: -1.09 (0.12), residues: 1534 loop : -1.45 (0.11), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.006 TRP H 245 HIS 0.013 0.003 HIS E 199 PHE 0.064 0.006 PHE Z 260 TYR 0.042 0.006 TYR R 110 ARG 0.010 0.001 ARG O 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1927 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 582 poor density : 1345 time to evaluate : 4.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8444 (mmmm) REVERT: A 42 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8061 (ptpt) REVERT: A 105 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8314 (tm-30) REVERT: A 125 GLN cc_start: 0.8221 (mt0) cc_final: 0.7627 (mm-40) REVERT: A 140 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8926 (mmp) REVERT: A 150 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8671 (pttm) REVERT: A 161 TRP cc_start: 0.8767 (t60) cc_final: 0.8451 (t-100) REVERT: A 184 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7559 (mmm160) REVERT: A 196 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8738 (tmtm) REVERT: A 197 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8251 (mt-10) REVERT: A 207 GLN cc_start: 0.8100 (mt0) cc_final: 0.7870 (mt0) REVERT: A 215 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8413 (mmmm) REVERT: A 217 LYS cc_start: 0.8599 (tttt) cc_final: 0.7876 (pttt) REVERT: B 3 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6965 (tp30) REVERT: B 31 THR cc_start: 0.9159 (p) cc_final: 0.8919 (t) REVERT: B 62 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8316 (mmmt) REVERT: B 87 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8565 (p) REVERT: B 118 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8038 (mt-10) REVERT: B 181 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7899 (mt-10) REVERT: B 182 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8623 (tp) REVERT: B 183 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7891 (mp0) REVERT: B 197 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: B 221 VAL cc_start: 0.7944 (m) cc_final: 0.7660 (t) REVERT: C 29 GLN cc_start: 0.8318 (mt0) cc_final: 0.8104 (mt0) REVERT: C 40 LYS cc_start: 0.8186 (mmtp) cc_final: 0.7760 (pttt) REVERT: C 130 TYR cc_start: 0.8911 (m-80) cc_final: 0.8582 (m-80) REVERT: C 161 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8022 (p0) REVERT: C 250 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8578 (m) REVERT: C 265 ARG cc_start: 0.7561 (tpp-160) cc_final: 0.7098 (tpt-90) REVERT: C 270 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6813 (mmtt) REVERT: D 4 ASP cc_start: 0.8367 (p0) cc_final: 0.8157 (p0) REVERT: D 52 LYS cc_start: 0.7705 (mttp) cc_final: 0.7420 (tptm) REVERT: D 61 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8481 (mmpt) REVERT: D 174 LYS cc_start: 0.8584 (mmmt) cc_final: 0.8286 (mtpt) REVERT: D 177 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8151 (mmtp) REVERT: D 178 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8124 (t70) REVERT: D 180 MET cc_start: 0.8346 (mtt) cc_final: 0.7947 (mtm) REVERT: D 215 ARG cc_start: 0.8395 (ttp-170) cc_final: 0.8038 (mtp-110) REVERT: D 224 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7948 (ptmt) REVERT: D 227 VAL cc_start: 0.8966 (t) cc_final: 0.8688 (p) REVERT: E 107 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6547 (mt-10) REVERT: E 109 ASP cc_start: 0.6384 (OUTLIER) cc_final: 0.5467 (m-30) REVERT: E 140 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8775 (mm) REVERT: E 171 ASP cc_start: 0.9112 (t0) cc_final: 0.8899 (t0) REVERT: E 190 GLU cc_start: 0.8464 (tp30) cc_final: 0.7961 (tp30) REVERT: E 220 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8766 (m) REVERT: E 221 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6546 (pp) REVERT: E 252 GLN cc_start: 0.8694 (mt0) cc_final: 0.8432 (mt0) REVERT: E 287 ARG cc_start: 0.8720 (ttp-110) cc_final: 0.8292 (mtt-85) REVERT: E 300 ASP cc_start: 0.8111 (m-30) cc_final: 0.7610 (m-30) REVERT: E 307 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6879 (pt0) REVERT: E 326 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8532 (mmtm) REVERT: E 328 HIS cc_start: 0.8373 (m-70) cc_final: 0.7910 (m-70) REVERT: E 342 MET cc_start: 0.6559 (OUTLIER) cc_final: 0.6140 (ttm) REVERT: F 203 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8871 (pttt) REVERT: F 220 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6761 (tp30) REVERT: F 221 LEU cc_start: 0.8087 (tt) cc_final: 0.7829 (tm) REVERT: F 237 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8816 (mtp) REVERT: F 270 MET cc_start: 0.9139 (mmm) cc_final: 0.8863 (mmm) REVERT: F 273 MET cc_start: 0.9089 (ttm) cc_final: 0.8753 (ttp) REVERT: F 276 MET cc_start: 0.8509 (mtt) cc_final: 0.8306 (mtm) REVERT: F 322 LYS cc_start: 0.8889 (mttp) cc_final: 0.8646 (mttt) REVERT: F 369 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7271 (mm-30) REVERT: F 371 ASN cc_start: 0.8466 (p0) cc_final: 0.8258 (p0) REVERT: F 382 LYS cc_start: 0.8806 (ttpp) cc_final: 0.8559 (ttpt) REVERT: F 395 ARG cc_start: 0.7530 (mtp180) cc_final: 0.7325 (mtm-85) REVERT: F 402 LYS cc_start: 0.7176 (tttp) cc_final: 0.6888 (tppt) REVERT: G 13 ASP cc_start: 0.8693 (p0) cc_final: 0.8462 (p0) REVERT: G 43 LYS cc_start: 0.8609 (mmtp) cc_final: 0.8014 (mtmt) REVERT: G 51 GLU cc_start: 0.8290 (tt0) cc_final: 0.8034 (pp20) REVERT: G 205 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7326 (ttmt) REVERT: G 231 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7477 (mpt) REVERT: H 105 ASP cc_start: 0.8890 (m-30) cc_final: 0.8583 (m-30) REVERT: H 123 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8339 (p0) REVERT: H 137 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.8878 (t80) REVERT: H 143 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7983 (mmp) REVERT: H 201 MET cc_start: 0.8877 (mtt) cc_final: 0.8618 (mtt) REVERT: H 234 ASP cc_start: 0.8680 (p0) cc_final: 0.8455 (p0) REVERT: H 274 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8828 (mt) REVERT: H 279 MET cc_start: 0.8890 (mtp) cc_final: 0.8673 (mtp) REVERT: I 66 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8742 (mmt) REVERT: I 71 MET cc_start: 0.9038 (mmm) cc_final: 0.8725 (mmt) REVERT: I 81 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.8923 (m) REVERT: I 85 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8773 (p) REVERT: I 118 ARG cc_start: 0.8818 (ttm170) cc_final: 0.8468 (mtm-85) REVERT: I 209 LYS cc_start: 0.9032 (tptt) cc_final: 0.8471 (tptt) REVERT: I 213 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: I 225 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6998 (mmp) REVERT: I 232 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7981 (mm) REVERT: J 4 MET cc_start: 0.9101 (mmm) cc_final: 0.8841 (mmt) REVERT: J 25 ASP cc_start: 0.8995 (p0) cc_final: 0.8744 (p0) REVERT: J 38 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8521 (mm-30) REVERT: J 75 LYS cc_start: 0.9141 (tmtm) cc_final: 0.8596 (tptt) REVERT: J 79 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8327 (mt-10) REVERT: J 81 ASP cc_start: 0.8731 (m-30) cc_final: 0.8423 (m-30) REVERT: J 90 MET cc_start: 0.9267 (ttp) cc_final: 0.9059 (ttt) REVERT: J 97 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8218 (mt-10) REVERT: J 114 LYS cc_start: 0.8035 (tttt) cc_final: 0.7545 (tppt) REVERT: J 193 ASP cc_start: 0.8190 (t70) cc_final: 0.7973 (t0) REVERT: J 201 LYS cc_start: 0.8938 (tttp) cc_final: 0.8567 (tptp) REVERT: K 1 MET cc_start: 0.7937 (mmm) cc_final: 0.7107 (mmm) REVERT: K 13 TYR cc_start: 0.9143 (p90) cc_final: 0.8887 (p90) REVERT: K 62 LYS cc_start: 0.8935 (tttm) cc_final: 0.8727 (tttm) REVERT: K 115 SER cc_start: 0.9120 (p) cc_final: 0.8893 (p) REVERT: K 129 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8351 (mtp) REVERT: K 145 TYR cc_start: 0.9187 (m-10) cc_final: 0.8883 (m-10) REVERT: K 163 SER cc_start: 0.8536 (OUTLIER) cc_final: 0.8310 (m) REVERT: K 200 GLU cc_start: 0.8920 (pt0) cc_final: 0.8637 (pt0) REVERT: K 206 HIS cc_start: 0.8279 (p90) cc_final: 0.7954 (p90) REVERT: L 155 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8690 (mt-10) REVERT: L 249 GLU cc_start: 0.8572 (tp30) cc_final: 0.8035 (mp0) REVERT: M 143 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8274 (p0) REVERT: M 152 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8565 (ttm170) REVERT: M 154 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8780 (p0) REVERT: M 174 TYR cc_start: 0.8704 (m-10) cc_final: 0.7992 (m-10) REVERT: M 182 MET cc_start: 0.9125 (ttt) cc_final: 0.8745 (ttt) REVERT: M 240 ASP cc_start: 0.8479 (p0) cc_final: 0.8221 (p0) REVERT: M 241 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7320 (mm-30) REVERT: M 311 ARG cc_start: 0.9168 (mmt180) cc_final: 0.8707 (mmt180) REVERT: M 317 ASP cc_start: 0.8358 (m-30) cc_final: 0.8098 (m-30) REVERT: M 337 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8540 (mtt-85) REVERT: M 338 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8306 (mmtp) REVERT: N 64 GLU cc_start: 0.8715 (tt0) cc_final: 0.8506 (tt0) REVERT: N 69 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8400 (mpt180) REVERT: N 96 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8980 (ppt170) REVERT: N 100 ASP cc_start: 0.8533 (t70) cc_final: 0.8171 (t0) REVERT: N 151 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8111 (pt0) REVERT: N 163 MET cc_start: 0.9024 (tpp) cc_final: 0.8818 (mmm) REVERT: N 179 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8631 (mtt-85) REVERT: N 183 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8437 (tppt) REVERT: N 211 TYR cc_start: 0.9207 (m-10) cc_final: 0.8797 (m-10) REVERT: O 42 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8440 (ptmt) REVERT: O 53 ILE cc_start: 0.8788 (pt) cc_final: 0.8461 (mm) REVERT: O 67 TYR cc_start: 0.9222 (m-80) cc_final: 0.8951 (m-80) REVERT: O 93 GLU cc_start: 0.8401 (tt0) cc_final: 0.8060 (mt-10) REVERT: O 115 MET cc_start: 0.9295 (mmm) cc_final: 0.9008 (mmp) REVERT: O 125 GLN cc_start: 0.8550 (mt0) cc_final: 0.8216 (mm-40) REVERT: O 193 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9029 (mt) REVERT: O 217 LYS cc_start: 0.8303 (tttt) cc_final: 0.7979 (pttm) REVERT: P 3 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6617 (tt0) REVERT: P 16 LYS cc_start: 0.8960 (ptmt) cc_final: 0.8258 (mmtm) REVERT: P 39 THR cc_start: 0.8826 (p) cc_final: 0.8414 (m) REVERT: P 42 VAL cc_start: 0.9446 (OUTLIER) cc_final: 0.9245 (p) REVERT: P 47 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8966 (ptmt) REVERT: P 62 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8362 (mmmt) REVERT: P 74 TYR cc_start: 0.9277 (p90) cc_final: 0.9065 (p90) REVERT: P 90 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8673 (tttm) REVERT: P 154 TRP cc_start: 0.7929 (m100) cc_final: 0.7035 (m-90) REVERT: P 167 ASP cc_start: 0.8411 (m-30) cc_final: 0.7963 (m-30) REVERT: P 174 LYS cc_start: 0.8283 (mttm) cc_final: 0.8071 (mtpp) REVERT: P 179 ASP cc_start: 0.7958 (m-30) cc_final: 0.7735 (m-30) REVERT: P 181 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7971 (mt-10) REVERT: P 197 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.6922 (t80) REVERT: P 201 MET cc_start: 0.8784 (mtm) cc_final: 0.8425 (mtm) REVERT: P 202 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8626 (t) REVERT: P 205 ASN cc_start: 0.8478 (t0) cc_final: 0.8228 (t0) REVERT: P 226 ASP cc_start: 0.7879 (m-30) cc_final: 0.7371 (t70) REVERT: Q 15 GLU cc_start: 0.8194 (tt0) cc_final: 0.7982 (mm-30) REVERT: Q 29 GLN cc_start: 0.8468 (mt0) cc_final: 0.8194 (mm110) REVERT: Q 64 LYS cc_start: 0.8475 (mmtm) cc_final: 0.8268 (mmtt) REVERT: Q 174 ASP cc_start: 0.7883 (p0) cc_final: 0.7272 (p0) REVERT: Q 182 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7638 (mttm) REVERT: Q 200 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8299 (mtp-110) REVERT: Q 204 LYS cc_start: 0.8548 (tttt) cc_final: 0.7867 (tptp) REVERT: Q 214 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8534 (m-30) REVERT: Q 237 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8439 (tptp) REVERT: Q 250 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8462 (p) REVERT: R 23 GLN cc_start: 0.8266 (mt0) cc_final: 0.7998 (mm-40) REVERT: R 47 LYS cc_start: 0.8448 (mttt) cc_final: 0.8244 (mtmm) REVERT: R 54 GLN cc_start: 0.8325 (pt0) cc_final: 0.7587 (mm-40) REVERT: R 60 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7837 (mpt90) REVERT: R 146 LYS cc_start: 0.8956 (tttm) cc_final: 0.8722 (tttp) REVERT: R 175 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8467 (t) REVERT: R 187 HIS cc_start: 0.8953 (t70) cc_final: 0.8718 (t-90) REVERT: R 213 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7902 (mp0) REVERT: R 218 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8273 (p) REVERT: R 219 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7672 (mm-30) REVERT: R 223 GLN cc_start: 0.7261 (mt0) cc_final: 0.7029 (tm-30) REVERT: R 232 GLU cc_start: 0.6996 (tt0) cc_final: 0.6618 (mt-10) REVERT: S 110 ARG cc_start: 0.7577 (mtt180) cc_final: 0.6724 (ptp-110) REVERT: S 221 ILE cc_start: 0.6611 (OUTLIER) cc_final: 0.6152 (pp) REVERT: S 248 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7935 (mm-30) REVERT: S 249 LYS cc_start: 0.8592 (mmtm) cc_final: 0.8183 (mmmt) REVERT: S 257 ASP cc_start: 0.8728 (m-30) cc_final: 0.8490 (m-30) REVERT: S 306 MET cc_start: 0.8470 (ptm) cc_final: 0.8223 (ptp) REVERT: S 336 LYS cc_start: 0.8097 (tttt) cc_final: 0.7582 (tppp) REVERT: T 169 GLU cc_start: 0.7613 (pm20) cc_final: 0.7323 (pt0) REVERT: T 205 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8389 (ttpp) REVERT: T 215 ARG cc_start: 0.7191 (ttt180) cc_final: 0.6892 (ttp-110) REVERT: T 220 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.6034 (mm-30) REVERT: T 237 MET cc_start: 0.9024 (ttp) cc_final: 0.8678 (ttp) REVERT: T 266 ASN cc_start: 0.8932 (t0) cc_final: 0.8657 (t0) REVERT: T 279 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8058 (mm-30) REVERT: T 343 HIS cc_start: 0.7299 (m90) cc_final: 0.7037 (m-70) REVERT: T 347 CYS cc_start: 0.8878 (m) cc_final: 0.8490 (m) REVERT: T 358 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8593 (mttp) REVERT: T 373 LYS cc_start: 0.8345 (ptpt) cc_final: 0.7843 (mmtp) REVERT: T 395 ARG cc_start: 0.7409 (mtp180) cc_final: 0.7184 (mtm-85) REVERT: T 396 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7853 (ttmt) REVERT: T 404 ARG cc_start: 0.5848 (OUTLIER) cc_final: 0.5395 (ppt170) REVERT: U 13 ASP cc_start: 0.8434 (p0) cc_final: 0.8231 (p0) REVERT: U 25 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8542 (mt-10) REVERT: U 29 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8372 (mttt) REVERT: U 86 ARG cc_start: 0.8954 (mtp180) cc_final: 0.8743 (mmm-85) REVERT: U 94 GLN cc_start: 0.8516 (tt0) cc_final: 0.8131 (tm-30) REVERT: U 115 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8657 (mmp80) REVERT: U 120 MET cc_start: 0.9106 (mtp) cc_final: 0.8906 (mtm) REVERT: U 141 TYR cc_start: 0.9396 (t80) cc_final: 0.9149 (t80) REVERT: U 192 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8059 (mttp) REVERT: U 203 LYS cc_start: 0.7938 (mttt) cc_final: 0.7445 (mtmm) REVERT: U 210 GLU cc_start: 0.8450 (pt0) cc_final: 0.8240 (pt0) REVERT: V 102 SER cc_start: 0.8599 (t) cc_final: 0.8260 (t) REVERT: V 139 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8355 (tptp) REVERT: V 140 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8579 (mtp) REVERT: V 143 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8067 (mmp) REVERT: V 201 MET cc_start: 0.8782 (mtt) cc_final: 0.8551 (mtm) REVERT: V 204 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8813 (p) REVERT: V 274 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8815 (mt) REVERT: W 61 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7596 (mtt180) REVERT: W 66 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8883 (mmt) REVERT: W 119 TYR cc_start: 0.9156 (m-80) cc_final: 0.8939 (m-80) REVERT: W 175 MET cc_start: 0.9391 (mtm) cc_final: 0.9138 (mtm) REVERT: W 182 GLU cc_start: 0.8674 (tp30) cc_final: 0.8380 (mm-30) REVERT: W 247 GLN cc_start: 0.8461 (mm110) cc_final: 0.8224 (mm-40) REVERT: X 6 TYR cc_start: 0.9021 (t80) cc_final: 0.8776 (t80) REVERT: X 12 MET cc_start: 0.9051 (tmm) cc_final: 0.8843 (tmm) REVERT: X 17 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8604 (ttmm) REVERT: X 30 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8416 (mt-10) REVERT: X 31 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8137 (mm-40) REVERT: X 38 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8567 (mm-30) REVERT: X 72 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8282 (mm-30) REVERT: X 93 SER cc_start: 0.9119 (OUTLIER) cc_final: 0.8687 (p) REVERT: X 99 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8678 (mmm160) REVERT: X 113 ASP cc_start: 0.8692 (t70) cc_final: 0.8444 (t70) REVERT: X 134 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8262 (pm20) REVERT: Y 1 MET cc_start: 0.7482 (mmm) cc_final: 0.7080 (mmm) REVERT: Y 15 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8833 (ttm) REVERT: Y 38 GLN cc_start: 0.9187 (tt0) cc_final: 0.8979 (tt0) REVERT: Y 40 ASP cc_start: 0.8564 (t0) cc_final: 0.8357 (t70) REVERT: Y 88 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8551 (t0) REVERT: Y 129 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8805 (mtm) REVERT: Y 156 ARG cc_start: 0.8979 (tpt-90) cc_final: 0.8688 (tpt90) REVERT: Y 200 GLU cc_start: 0.8755 (pt0) cc_final: 0.8256 (pm20) REVERT: Z 166 GLU cc_start: 0.8573 (tt0) cc_final: 0.8347 (tt0) REVERT: Z 194 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8811 (mt) REVERT: Z 196 MET cc_start: 0.9088 (ptm) cc_final: 0.8847 (ptp) REVERT: Z 244 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8302 (mmmt) REVERT: Z 280 GLU cc_start: 0.8305 (pt0) cc_final: 0.7870 (pm20) REVERT: Z 281 LYS cc_start: 0.8601 (mttm) cc_final: 0.8321 (mtmt) REVERT: a 131 ASP cc_start: 0.9160 (t0) cc_final: 0.8805 (t70) REVERT: a 152 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8558 (ttm170) REVERT: a 159 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8925 (pp) REVERT: a 192 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8386 (mmp) REVERT: a 226 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8537 (ptm160) REVERT: a 231 TYR cc_start: 0.9035 (t80) cc_final: 0.8777 (t80) REVERT: a 292 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8432 (ttp) REVERT: a 295 GLU cc_start: 0.8481 (mp0) cc_final: 0.8260 (mp0) REVERT: a 310 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8588 (mm-30) REVERT: a 312 ASP cc_start: 0.8561 (t0) cc_final: 0.8336 (t0) REVERT: a 337 ARG cc_start: 0.8867 (mtt-85) cc_final: 0.8642 (mtp85) REVERT: b 39 ARG cc_start: 0.8592 (ttm170) cc_final: 0.8264 (ttm170) REVERT: b 71 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8327 (ttpt) REVERT: b 77 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.7934 (m-30) REVERT: b 94 GLN cc_start: 0.8760 (tp40) cc_final: 0.8467 (tp-100) REVERT: b 96 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8866 (ppt170) REVERT: b 115 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7579 (tm-30) REVERT: b 122 ASP cc_start: 0.8647 (m-30) cc_final: 0.8409 (m-30) REVERT: b 151 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: b 179 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8810 (mmt90) outliers start: 582 outliers final: 150 residues processed: 1727 average time/residue: 1.4823 time to fit residues: 3123.8230 Evaluate side-chains 1257 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1003 time to evaluate : 4.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 149 PRO Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain D residue 12 PRO Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain H residue 173 SER Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 274 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 172 LYS Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 192 LYS Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 218 SER Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 152 ARG Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 159 LEU Chi-restraints excluded: chain M residue 219 SER Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 241 GLU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain M residue 337 ARG Chi-restraints excluded: chain M residue 338 LYS Chi-restraints excluded: chain N residue 3 SER Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 183 LYS Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 233 ARG Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 47 LYS Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 90 LYS Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 182 LYS Chi-restraints excluded: chain Q residue 200 ARG Chi-restraints excluded: chain Q residue 211 ILE Chi-restraints excluded: chain Q residue 214 ASP Chi-restraints excluded: chain Q residue 237 LYS Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 221 ILE Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 319 VAL Chi-restraints excluded: chain T residue 172 SER Chi-restraints excluded: chain T residue 220 GLU Chi-restraints excluded: chain T residue 235 VAL Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 358 LYS Chi-restraints excluded: chain T residue 362 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 396 LYS Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 192 LYS Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 123 ASP Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 140 MET Chi-restraints excluded: chain V residue 143 MET Chi-restraints excluded: chain V residue 173 SER Chi-restraints excluded: chain V residue 204 SER Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 274 ILE Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain W residue 167 LEU Chi-restraints excluded: chain W residue 237 THR Chi-restraints excluded: chain X residue 30 GLU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 99 ARG Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 15 MET Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 88 ASN Chi-restraints excluded: chain Y residue 97 ARG Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 129 MET Chi-restraints excluded: chain Y residue 181 ARG Chi-restraints excluded: chain Z residue 102 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 144 LEU Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 218 SER Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain a residue 143 ASP Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 152 ARG Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 167 LYS Chi-restraints excluded: chain a residue 192 MET Chi-restraints excluded: chain a residue 226 ARG Chi-restraints excluded: chain a residue 292 MET Chi-restraints excluded: chain a residue 310 GLU Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 96 ARG Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 179 ARG Chi-restraints excluded: chain b residue 192 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 520 optimal weight: 0.9990 chunk 466 optimal weight: 1.9990 chunk 259 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 314 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 482 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 293 optimal weight: 4.9990 chunk 359 optimal weight: 3.9990 chunk 559 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN B 100 ASN B 107 GLN B 117 GLN B 121 GLN B 187 HIS B 230 GLN C 239 HIS C 257 HIS C 263 GLN D 115 GLN D 120 GLN D 223 GLN E 199 HIS E 255 GLN E 278 GLN F 195 ASN F 225 GLN F 259 ASN F 286 GLN F 305 GLN F 311 GLN G 8 HIS G 147 GLN H 216 HIS H 246 ASN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 166 GLN I 201 GLN J 26 ASN J 65 ASN K 73 HIS K 84 ASN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 GLN K 186 ASN L 222 GLN L 291 GLN M 130 GLN M 180 ASN M 188 GLN M 204 ASN M 234 ASN M 330 GLN N 75 ASN N 153 ASN N 205 HIS O 174 GLN O 207 GLN O 228 ASN P 19 GLN P 93 GLN P 94 GLN P 100 ASN P 117 GLN P 121 GLN P 230 GLN Q 20 GLN Q 239 HIS R 18 GLN R 92 GLN R 115 GLN R 187 HIS S 314 ASN T 206 ASN T 271 ASN T 305 GLN T 331 GLN U 8 HIS U 54 HIS U 201 HIS V 147 ASN V 216 HIS V 241 GLN V 246 ASN W 86 ASN W 95 HIS W 102 GLN W 166 GLN W 247 GLN X 26 ASN X 65 ASN X 68 GLN Y 56 ASN Y 72 GLN Y 84 ASN Y 165 GLN Y 186 ASN ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN a 130 GLN a 180 ASN a 188 GLN b 62 GLN b 105 GLN Total number of N/Q/H flips: 93 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 50122 Z= 0.235 Angle : 0.594 9.377 67810 Z= 0.323 Chirality : 0.044 0.170 7544 Planarity : 0.004 0.045 8790 Dihedral : 11.030 95.618 7583 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.65 % Favored : 98.19 % Rotamer: Outliers : 6.62 % Allowed : 16.91 % Favored : 76.46 % 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: -0.03 (0.10), residues: 6290 helix: 1.03 (0.10), residues: 2336 sheet: -0.52 (0.12), residues: 1574 loop : -0.58 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 154 HIS 0.006 0.001 HIS D 187 PHE 0.019 0.002 PHE K 8 TYR 0.025 0.001 TYR W 119 ARG 0.006 0.001 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1472 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 1125 time to evaluate : 4.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8247 (mmmm) REVERT: A 42 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7803 (ptmm) REVERT: A 53 ILE cc_start: 0.8766 (pt) cc_final: 0.8442 (pp) REVERT: A 105 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8393 (tm-30) REVERT: A 115 MET cc_start: 0.9113 (mmm) cc_final: 0.8868 (mmm) REVERT: A 125 GLN cc_start: 0.8212 (mt0) cc_final: 0.7657 (mm-40) REVERT: A 161 TRP cc_start: 0.8740 (t60) cc_final: 0.8436 (t-100) REVERT: A 184 ARG cc_start: 0.7671 (tpp80) cc_final: 0.7421 (mmm160) REVERT: A 215 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8009 (mmmt) REVERT: A 217 LYS cc_start: 0.8664 (tttt) cc_final: 0.7995 (pttp) REVERT: A 223 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8639 (ttm170) REVERT: B 118 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8157 (tt0) REVERT: B 175 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7834 (mmt-90) REVERT: B 179 ASP cc_start: 0.8285 (m-30) cc_final: 0.7968 (m-30) REVERT: B 225 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7734 (mtm-85) REVERT: C 40 LYS cc_start: 0.8356 (mmtp) cc_final: 0.7854 (pttt) REVERT: C 130 TYR cc_start: 0.8609 (m-80) cc_final: 0.8341 (m-80) REVERT: C 196 LEU cc_start: 0.9048 (tp) cc_final: 0.8847 (tt) REVERT: C 207 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8226 (t0) REVERT: C 230 ASP cc_start: 0.8598 (m-30) cc_final: 0.8343 (m-30) REVERT: C 237 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8121 (tppt) REVERT: C 265 ARG cc_start: 0.7609 (tpp-160) cc_final: 0.7203 (tpt-90) REVERT: D 4 ASP cc_start: 0.8372 (p0) cc_final: 0.8046 (p0) REVERT: D 52 LYS cc_start: 0.7981 (mttp) cc_final: 0.7663 (mppt) REVERT: D 57 ARG cc_start: 0.7624 (tmm160) cc_final: 0.7184 (ptt90) REVERT: D 61 LYS cc_start: 0.8764 (mptp) cc_final: 0.8448 (mmpt) REVERT: D 99 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: D 121 SER cc_start: 0.8902 (m) cc_final: 0.8646 (p) REVERT: D 174 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8237 (mtpt) REVERT: D 177 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8075 (mmtp) REVERT: D 178 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8073 (t70) REVERT: D 180 MET cc_start: 0.8249 (mtt) cc_final: 0.7906 (mtm) REVERT: D 215 ARG cc_start: 0.8440 (ttp-170) cc_final: 0.8036 (mtp-110) REVERT: D 221 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7172 (tp30) REVERT: D 224 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7835 (ttpt) REVERT: D 232 GLU cc_start: 0.7403 (tt0) cc_final: 0.6964 (mt-10) REVERT: E 107 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6587 (mm-30) REVERT: E 109 ASP cc_start: 0.6928 (OUTLIER) cc_final: 0.5985 (m-30) REVERT: E 190 GLU cc_start: 0.8431 (tp30) cc_final: 0.7977 (tp30) REVERT: E 283 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: E 300 ASP cc_start: 0.7978 (m-30) cc_final: 0.7545 (m-30) REVERT: E 326 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8384 (mmtm) REVERT: E 328 HIS cc_start: 0.8511 (m-70) cc_final: 0.8145 (m-70) REVERT: E 342 MET cc_start: 0.6274 (ttm) cc_final: 0.5902 (ttm) REVERT: F 220 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6859 (tp30) REVERT: F 221 LEU cc_start: 0.7964 (tt) cc_final: 0.7730 (tm) REVERT: F 270 MET cc_start: 0.8967 (mmm) cc_final: 0.8557 (mmm) REVERT: F 371 ASN cc_start: 0.8274 (p0) cc_final: 0.8044 (p0) REVERT: G 43 LYS cc_start: 0.8625 (mmtp) cc_final: 0.8374 (mmmt) REVERT: G 51 GLU cc_start: 0.8267 (tt0) cc_final: 0.7808 (pp20) REVERT: G 115 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8243 (mpt-90) REVERT: G 231 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7210 (mpt) REVERT: H 123 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8605 (t0) REVERT: H 139 LYS cc_start: 0.8807 (ttmm) cc_final: 0.8408 (ttpp) REVERT: H 143 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8023 (tpp) REVERT: H 201 MET cc_start: 0.8941 (mtt) cc_final: 0.8657 (mtt) REVERT: I 51 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7894 (tp30) REVERT: I 71 MET cc_start: 0.8761 (mmm) cc_final: 0.8479 (mmp) REVERT: I 213 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: J 4 MET cc_start: 0.9147 (mmm) cc_final: 0.8919 (mmt) REVERT: J 38 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8544 (mm-30) REVERT: J 48 SER cc_start: 0.9168 (p) cc_final: 0.8922 (m) REVERT: J 75 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8474 (mmtt) REVERT: J 79 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: J 81 ASP cc_start: 0.8582 (m-30) cc_final: 0.8381 (m-30) REVERT: J 97 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8155 (mt-10) REVERT: J 114 LYS cc_start: 0.7941 (tttt) cc_final: 0.7516 (tppt) REVERT: J 198 ARG cc_start: 0.9151 (mtt90) cc_final: 0.8918 (mtt180) REVERT: J 201 LYS cc_start: 0.9116 (tttp) cc_final: 0.8603 (ttpt) REVERT: K 1 MET cc_start: 0.7859 (mmm) cc_final: 0.7246 (mmm) REVERT: K 11 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8799 (tttm) REVERT: K 13 TYR cc_start: 0.9088 (p90) cc_final: 0.8731 (p90) REVERT: K 101 TYR cc_start: 0.8876 (m-80) cc_final: 0.8662 (m-80) REVERT: K 196 LYS cc_start: 0.8731 (ptmm) cc_final: 0.8467 (ptmm) REVERT: K 200 GLU cc_start: 0.9014 (pt0) cc_final: 0.8686 (pt0) REVERT: K 203 THR cc_start: 0.8258 (m) cc_final: 0.8045 (p) REVERT: K 206 HIS cc_start: 0.8251 (p90) cc_final: 0.7974 (p-80) REVERT: L 134 LEU cc_start: 0.9101 (tt) cc_final: 0.8456 (mp) REVERT: L 155 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8281 (mp0) REVERT: L 190 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8483 (ptt-90) REVERT: L 191 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.7854 (m110) REVERT: M 130 GLN cc_start: 0.8511 (tt0) cc_final: 0.8298 (tt0) REVERT: M 152 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8386 (ttm170) REVERT: M 174 TYR cc_start: 0.8755 (m-10) cc_final: 0.7964 (m-10) REVERT: M 182 MET cc_start: 0.8908 (ttt) cc_final: 0.8641 (ttt) REVERT: M 226 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7099 (ptp-170) REVERT: M 281 ARG cc_start: 0.8549 (mtp85) cc_final: 0.7743 (mtp-110) REVERT: M 330 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7507 (tm130) REVERT: M 338 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8170 (mmtm) REVERT: N 69 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8122 (mtt90) REVERT: N 100 ASP cc_start: 0.8089 (t70) cc_final: 0.7791 (t0) REVERT: N 148 GLN cc_start: 0.9004 (tt0) cc_final: 0.8686 (tt0) REVERT: N 163 MET cc_start: 0.8942 (tpp) cc_final: 0.8728 (mmm) REVERT: N 179 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8609 (mtt90) REVERT: N 183 LYS cc_start: 0.8963 (ttpt) cc_final: 0.8490 (tppt) REVERT: N 203 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: O 7 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7274 (p0) REVERT: O 67 TYR cc_start: 0.9115 (m-80) cc_final: 0.8845 (m-80) REVERT: O 93 GLU cc_start: 0.8253 (tt0) cc_final: 0.7723 (mt-10) REVERT: O 115 MET cc_start: 0.9169 (mmm) cc_final: 0.8948 (mmp) REVERT: O 125 GLN cc_start: 0.8384 (mt0) cc_final: 0.8090 (mm-40) REVERT: O 140 MET cc_start: 0.9406 (mmm) cc_final: 0.9151 (mmm) REVERT: O 172 LYS cc_start: 0.8620 (tptt) cc_final: 0.8381 (tptp) REVERT: O 178 MET cc_start: 0.9216 (mmp) cc_final: 0.8929 (tpt) REVERT: O 186 LYS cc_start: 0.8480 (mttt) cc_final: 0.8227 (mttt) REVERT: O 190 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8315 (mp) REVERT: O 217 LYS cc_start: 0.8439 (tttt) cc_final: 0.8149 (pttp) REVERT: P 16 LYS cc_start: 0.8907 (ptmt) cc_final: 0.8144 (mmtt) REVERT: P 39 THR cc_start: 0.8863 (p) cc_final: 0.8421 (m) REVERT: P 90 LYS cc_start: 0.8908 (ttmt) cc_final: 0.8684 (tttm) REVERT: P 154 TRP cc_start: 0.8052 (m100) cc_final: 0.6920 (m-90) REVERT: P 171 PHE cc_start: 0.8554 (t80) cc_final: 0.8179 (t80) REVERT: P 197 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.6951 (t80) REVERT: P 202 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8568 (t) REVERT: P 220 SER cc_start: 0.8446 (p) cc_final: 0.8232 (m) REVERT: P 226 ASP cc_start: 0.7892 (m-30) cc_final: 0.7606 (t70) REVERT: Q 15 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: Q 29 GLN cc_start: 0.8348 (mt0) cc_final: 0.8027 (mt0) REVERT: Q 53 HIS cc_start: 0.8648 (t-90) cc_final: 0.8202 (t-90) REVERT: Q 190 THR cc_start: 0.8764 (p) cc_final: 0.8545 (p) REVERT: Q 193 ASP cc_start: 0.8522 (t0) cc_final: 0.8280 (m-30) REVERT: Q 204 LYS cc_start: 0.8374 (tttt) cc_final: 0.7968 (tptp) REVERT: R 23 GLN cc_start: 0.8098 (mt0) cc_final: 0.7854 (mm-40) REVERT: R 54 GLN cc_start: 0.8348 (pt0) cc_final: 0.7595 (mm-40) REVERT: R 60 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7936 (mpt90) REVERT: R 141 LYS cc_start: 0.8157 (tptt) cc_final: 0.7922 (tppp) REVERT: R 152 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8561 (tmt) REVERT: R 206 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8180 (tt) REVERT: R 213 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7881 (mp0) REVERT: R 218 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8379 (p) REVERT: R 220 GLU cc_start: 0.7458 (pm20) cc_final: 0.7098 (pm20) REVERT: S 110 ARG cc_start: 0.7530 (mtt180) cc_final: 0.6901 (mtm110) REVERT: S 118 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8370 (mp0) REVERT: S 249 LYS cc_start: 0.8604 (mmtm) cc_final: 0.8220 (mmmt) REVERT: S 257 ASP cc_start: 0.8714 (m-30) cc_final: 0.8490 (m-30) REVERT: S 275 GLU cc_start: 0.8496 (pm20) cc_final: 0.8267 (pm20) REVERT: S 289 MET cc_start: 0.8957 (mtt) cc_final: 0.8702 (mtp) REVERT: S 300 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8135 (m-30) REVERT: S 306 MET cc_start: 0.8172 (ptm) cc_final: 0.7884 (ptp) REVERT: S 309 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8381 (mm110) REVERT: S 336 LYS cc_start: 0.8117 (tttt) cc_final: 0.7627 (tppp) REVERT: T 279 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8003 (mm-30) REVERT: T 343 HIS cc_start: 0.7281 (m90) cc_final: 0.6940 (m-70) REVERT: T 347 CYS cc_start: 0.8737 (m) cc_final: 0.8389 (m) REVERT: T 401 PHE cc_start: 0.7557 (t80) cc_final: 0.7249 (t80) REVERT: T 404 ARG cc_start: 0.5860 (OUTLIER) cc_final: 0.5313 (ppt170) REVERT: U 29 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8201 (mtmt) REVERT: U 61 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8341 (tptp) REVERT: U 86 ARG cc_start: 0.8773 (mtp180) cc_final: 0.8540 (mmm-85) REVERT: U 94 GLN cc_start: 0.8488 (tt0) cc_final: 0.8155 (tm-30) REVERT: U 115 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8343 (mmt90) REVERT: U 203 LYS cc_start: 0.7862 (mttt) cc_final: 0.7376 (mtmm) REVERT: V 140 MET cc_start: 0.8578 (mtp) cc_final: 0.8373 (mtp) REVERT: V 143 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8161 (mmp) REVERT: V 201 MET cc_start: 0.8813 (mtt) cc_final: 0.8476 (mtm) REVERT: V 273 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8181 (tppt) REVERT: W 61 ARG cc_start: 0.7761 (mtp85) cc_final: 0.7437 (mmt180) REVERT: W 85 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.9084 (m) REVERT: W 119 TYR cc_start: 0.9052 (m-80) cc_final: 0.8679 (m-80) REVERT: W 149 ASP cc_start: 0.8058 (m-30) cc_final: 0.7739 (m-30) REVERT: X 6 TYR cc_start: 0.9043 (t80) cc_final: 0.8772 (t80) REVERT: X 14 MET cc_start: 0.8774 (mtt) cc_final: 0.8528 (mtt) REVERT: X 38 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8635 (mm-30) REVERT: X 134 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: Y 38 GLN cc_start: 0.9189 (tt0) cc_final: 0.8948 (tt0) REVERT: Y 118 ASP cc_start: 0.8896 (t0) cc_final: 0.8689 (t0) REVERT: Y 145 TYR cc_start: 0.8879 (m-80) cc_final: 0.8523 (m-80) REVERT: Y 200 GLU cc_start: 0.8751 (pt0) cc_final: 0.8226 (pm20) REVERT: Z 131 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8190 (mmt) REVERT: Z 191 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.7845 (m110) REVERT: Z 194 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8400 (mp) REVERT: Z 244 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8454 (mttm) REVERT: Z 281 LYS cc_start: 0.8658 (mttm) cc_final: 0.8315 (mtmt) REVERT: Z 291 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8659 (pp30) REVERT: a 152 ARG cc_start: 0.9287 (OUTLIER) cc_final: 0.8767 (ttm170) REVERT: a 201 LYS cc_start: 0.8853 (mtpm) cc_final: 0.8613 (ttpm) REVERT: a 242 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8081 (mm-30) REVERT: a 295 GLU cc_start: 0.8444 (mp0) cc_final: 0.8213 (mp0) REVERT: a 337 ARG cc_start: 0.8835 (mtt-85) cc_final: 0.8616 (mtp85) REVERT: b 77 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8109 (m-30) REVERT: b 115 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7680 (tm-30) REVERT: b 151 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: b 179 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8707 (mmt90) outliers start: 347 outliers final: 103 residues processed: 1340 average time/residue: 1.3977 time to fit residues: 2301.9488 Evaluate side-chains 1129 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 967 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 190 ARG Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 152 ARG Chi-restraints excluded: chain M residue 159 LEU Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 330 GLN Chi-restraints excluded: chain M residue 338 LYS Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 172 GLN Chi-restraints excluded: chain Q residue 187 GLU Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 300 ASP Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 61 LYS Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 195 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 143 MET Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 85 THR Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain W residue 210 ASP Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 152 GLN Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain Z residue 291 GLN Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 152 ARG Chi-restraints excluded: chain a residue 157 PHE Chi-restraints excluded: chain a residue 253 VAL Chi-restraints excluded: chain a residue 327 ASP Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 179 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 310 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 465 optimal weight: 5.9990 chunk 380 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 560 optimal weight: 0.6980 chunk 605 optimal weight: 0.9990 chunk 499 optimal weight: 3.9990 chunk 555 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 449 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 205 ASN C 62 GLN D 18 GLN D 97 ASN D 187 HIS E 113 ASN F 190 ASN F 225 GLN F 259 ASN F 305 GLN G 8 HIS G 98 ASN G 147 GLN I 95 HIS K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 GLN L 291 GLN M 180 ASN O 228 ASN P 19 GLN P 107 GLN P 205 ASN Q 20 GLN R 143 HIS T 266 ASN T 305 GLN U 64 ASN V 241 GLN W 115 HIS X 169 GLN Y 22 ASN Y 72 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN a 180 ASN b 94 GLN b 105 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 50122 Z= 0.261 Angle : 0.553 8.987 67810 Z= 0.298 Chirality : 0.043 0.192 7544 Planarity : 0.004 0.052 8790 Dihedral : 8.659 88.437 7243 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.91 % Favored : 98.00 % Rotamer: Outliers : 5.19 % Allowed : 19.40 % Favored : 75.41 % 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: 0.62 (0.10), residues: 6290 helix: 1.72 (0.10), residues: 2356 sheet: -0.26 (0.12), residues: 1574 loop : -0.34 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 165 HIS 0.007 0.001 HIS R 187 PHE 0.018 0.002 PHE Y 8 TYR 0.020 0.001 TYR W 119 ARG 0.008 0.000 ARG b 195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1295 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1023 time to evaluate : 4.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7839 (ptpt) REVERT: A 53 ILE cc_start: 0.8741 (pt) cc_final: 0.8444 (pp) REVERT: A 125 GLN cc_start: 0.8157 (mt0) cc_final: 0.7697 (mm-40) REVERT: A 161 TRP cc_start: 0.8743 (t60) cc_final: 0.8337 (t-100) REVERT: A 184 ARG cc_start: 0.7764 (tpp80) cc_final: 0.7418 (mmm160) REVERT: A 215 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8132 (mmtt) REVERT: A 217 LYS cc_start: 0.8696 (tttt) cc_final: 0.8033 (pttp) REVERT: A 232 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8167 (tp40) REVERT: B 3 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.5419 (tm-30) REVERT: B 87 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8481 (m) REVERT: B 175 ARG cc_start: 0.8295 (mmm160) cc_final: 0.8039 (mmm160) REVERT: B 179 ASP cc_start: 0.8158 (m-30) cc_final: 0.7890 (m-30) REVERT: B 184 ASP cc_start: 0.7661 (t0) cc_final: 0.7401 (m-30) REVERT: C 40 LYS cc_start: 0.8454 (mmtp) cc_final: 0.7925 (pttt) REVERT: C 130 TYR cc_start: 0.8570 (m-80) cc_final: 0.8320 (m-80) REVERT: C 207 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8191 (t0) REVERT: C 230 ASP cc_start: 0.8561 (m-30) cc_final: 0.8222 (m-30) REVERT: C 237 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8270 (tppt) REVERT: C 265 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7462 (tpt-90) REVERT: D 4 ASP cc_start: 0.8363 (p0) cc_final: 0.8089 (p0) REVERT: D 52 LYS cc_start: 0.8062 (mttp) cc_final: 0.7678 (mppt) REVERT: D 57 ARG cc_start: 0.7748 (tmm160) cc_final: 0.7275 (ptt90) REVERT: D 61 LYS cc_start: 0.8775 (mptp) cc_final: 0.8464 (mmpt) REVERT: D 121 SER cc_start: 0.8852 (m) cc_final: 0.8624 (p) REVERT: D 174 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8287 (mtpt) REVERT: D 177 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8042 (mmtp) REVERT: D 178 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8102 (t70) REVERT: D 180 MET cc_start: 0.8254 (mtt) cc_final: 0.7884 (mtm) REVERT: D 215 ARG cc_start: 0.8451 (ttp-170) cc_final: 0.8029 (mtp-110) REVERT: D 221 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7200 (tp30) REVERT: D 232 GLU cc_start: 0.7445 (tt0) cc_final: 0.6967 (mt-10) REVERT: E 107 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: E 109 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.5906 (m-30) REVERT: E 190 GLU cc_start: 0.8421 (tp30) cc_final: 0.8018 (tp30) REVERT: E 278 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7582 (mt0) REVERT: E 287 ARG cc_start: 0.8821 (ttp-110) cc_final: 0.8429 (mtm-85) REVERT: E 300 ASP cc_start: 0.8004 (m-30) cc_final: 0.7544 (m-30) REVERT: E 326 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8395 (mmtm) REVERT: E 328 HIS cc_start: 0.8500 (m-70) cc_final: 0.8206 (m90) REVERT: E 342 MET cc_start: 0.6279 (ttm) cc_final: 0.5903 (ttm) REVERT: F 220 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6791 (tp30) REVERT: F 221 LEU cc_start: 0.7777 (tt) cc_final: 0.7553 (tm) REVERT: F 270 MET cc_start: 0.8973 (mmm) cc_final: 0.8583 (mmm) REVERT: F 402 LYS cc_start: 0.7075 (mmtm) cc_final: 0.6808 (mmmt) REVERT: G 43 LYS cc_start: 0.8657 (mmtp) cc_final: 0.8417 (mmmt) REVERT: G 51 GLU cc_start: 0.8279 (tt0) cc_final: 0.7780 (pp20) REVERT: G 115 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8214 (mpt-90) REVERT: G 184 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7536 (pt) REVERT: H 139 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8370 (ttpp) REVERT: H 143 MET cc_start: 0.8239 (ttp) cc_final: 0.8017 (tpp) REVERT: H 201 MET cc_start: 0.8884 (mtt) cc_final: 0.8619 (mtt) REVERT: H 279 MET cc_start: 0.8937 (mtm) cc_final: 0.8477 (mtp) REVERT: I 101 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8558 (mttp) REVERT: I 213 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: I 225 MET cc_start: 0.7369 (mtp) cc_final: 0.7000 (mtt) REVERT: I 226 TYR cc_start: 0.7091 (t80) cc_final: 0.6440 (t80) REVERT: I 230 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: J 4 MET cc_start: 0.9142 (mmm) cc_final: 0.8859 (mmt) REVERT: J 38 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8545 (mm-30) REVERT: J 48 SER cc_start: 0.9157 (p) cc_final: 0.8935 (m) REVERT: J 79 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: J 97 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8199 (mt-10) REVERT: J 114 LYS cc_start: 0.8062 (tttt) cc_final: 0.7527 (tppt) REVERT: J 201 LYS cc_start: 0.9095 (tttp) cc_final: 0.8558 (ttpt) REVERT: K 1 MET cc_start: 0.7601 (mmm) cc_final: 0.7105 (mmm) REVERT: K 101 TYR cc_start: 0.8951 (m-80) cc_final: 0.8718 (m-80) REVERT: K 196 LYS cc_start: 0.8742 (ptmm) cc_final: 0.8466 (ptmm) REVERT: K 200 GLU cc_start: 0.8988 (pt0) cc_final: 0.8627 (pt0) REVERT: K 206 HIS cc_start: 0.8271 (p90) cc_final: 0.8017 (p-80) REVERT: L 155 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: L 190 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8490 (ptt-90) REVERT: L 191 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.7812 (m110) REVERT: M 152 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8516 (ttm170) REVERT: M 174 TYR cc_start: 0.8760 (m-10) cc_final: 0.7924 (m-10) REVERT: M 212 LYS cc_start: 0.9038 (tttm) cc_final: 0.8775 (ttpp) REVERT: M 226 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7310 (ptp-170) REVERT: M 281 ARG cc_start: 0.8446 (mtp85) cc_final: 0.7591 (mtp-110) REVERT: M 332 GLU cc_start: 0.8236 (pt0) cc_final: 0.8024 (pt0) REVERT: M 335 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8574 (mm-30) REVERT: M 338 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8349 (mmtm) REVERT: N 69 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8048 (mtt90) REVERT: N 100 ASP cc_start: 0.8080 (t70) cc_final: 0.7803 (t0) REVERT: N 106 MET cc_start: 0.8886 (mpt) cc_final: 0.8256 (mpt) REVERT: N 148 GLN cc_start: 0.8988 (tt0) cc_final: 0.8650 (tt0) REVERT: N 179 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8589 (mtt-85) REVERT: N 195 ARG cc_start: 0.8677 (mtp-110) cc_final: 0.8225 (mtp180) REVERT: N 203 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: O 7 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7251 (p0) REVERT: O 67 TYR cc_start: 0.9103 (m-80) cc_final: 0.8802 (m-80) REVERT: O 93 GLU cc_start: 0.8183 (tt0) cc_final: 0.7941 (tm-30) REVERT: O 115 MET cc_start: 0.9201 (mmm) cc_final: 0.8976 (mmp) REVERT: O 125 GLN cc_start: 0.8315 (mt0) cc_final: 0.8099 (tt0) REVERT: O 140 MET cc_start: 0.9388 (mmm) cc_final: 0.9180 (mmm) REVERT: O 186 LYS cc_start: 0.8462 (mttt) cc_final: 0.8217 (mttt) REVERT: O 190 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8389 (mp) REVERT: O 217 LYS cc_start: 0.8469 (tttt) cc_final: 0.8205 (pttp) REVERT: P 16 LYS cc_start: 0.8893 (ptmt) cc_final: 0.8137 (mmtm) REVERT: P 154 TRP cc_start: 0.7951 (m100) cc_final: 0.6873 (m-90) REVERT: P 197 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.6701 (t80) REVERT: P 202 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8547 (t) REVERT: P 226 ASP cc_start: 0.7884 (m-30) cc_final: 0.7617 (t70) REVERT: Q 15 GLU cc_start: 0.8165 (tt0) cc_final: 0.7891 (tt0) REVERT: Q 29 GLN cc_start: 0.8280 (mt0) cc_final: 0.7926 (mt0) REVERT: Q 53 HIS cc_start: 0.8699 (t-90) cc_final: 0.8281 (t-90) REVERT: Q 193 ASP cc_start: 0.8457 (t0) cc_final: 0.8187 (m-30) REVERT: Q 204 LYS cc_start: 0.8560 (tttt) cc_final: 0.8142 (tptp) REVERT: R 23 GLN cc_start: 0.8213 (mt0) cc_final: 0.7903 (mm-40) REVERT: R 49 SER cc_start: 0.6302 (t) cc_final: 0.5824 (p) REVERT: R 54 GLN cc_start: 0.8306 (pt0) cc_final: 0.7590 (mm110) REVERT: R 60 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7883 (mpt90) REVERT: R 141 LYS cc_start: 0.8185 (tptt) cc_final: 0.7887 (tppp) REVERT: R 213 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7901 (mp0) REVERT: R 218 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8417 (p) REVERT: R 219 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: R 220 GLU cc_start: 0.7478 (pm20) cc_final: 0.7153 (pm20) REVERT: S 110 ARG cc_start: 0.7604 (mtt180) cc_final: 0.6873 (mtm110) REVERT: S 118 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8291 (mp0) REVERT: S 249 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8315 (mmmt) REVERT: S 306 MET cc_start: 0.8152 (ptm) cc_final: 0.7909 (ptp) REVERT: S 336 LYS cc_start: 0.8078 (tttt) cc_final: 0.7599 (tppp) REVERT: T 190 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7697 (m-40) REVERT: T 279 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8020 (mm-30) REVERT: T 290 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8329 (mttt) REVERT: T 343 HIS cc_start: 0.7326 (m90) cc_final: 0.7001 (m-70) REVERT: T 347 CYS cc_start: 0.8739 (m) cc_final: 0.8422 (m) REVERT: T 404 ARG cc_start: 0.5628 (OUTLIER) cc_final: 0.5253 (ppt170) REVERT: U 29 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8250 (mtmt) REVERT: U 86 ARG cc_start: 0.8747 (mtp180) cc_final: 0.8503 (mmm-85) REVERT: U 94 GLN cc_start: 0.8535 (tt0) cc_final: 0.8235 (tm-30) REVERT: U 115 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8348 (mmt90) REVERT: U 203 LYS cc_start: 0.7941 (mttt) cc_final: 0.7434 (mtmm) REVERT: V 140 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8347 (mtp) REVERT: V 143 MET cc_start: 0.8534 (ttp) cc_final: 0.8166 (mmp) REVERT: V 201 MET cc_start: 0.8823 (mtt) cc_final: 0.8546 (mtm) REVERT: V 273 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8189 (tppt) REVERT: W 61 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7490 (mmt90) REVERT: W 82 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: W 118 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8543 (ttt-90) REVERT: W 119 TYR cc_start: 0.8937 (m-80) cc_final: 0.8649 (m-80) REVERT: W 149 ASP cc_start: 0.8169 (m-30) cc_final: 0.7818 (m-30) REVERT: X 6 TYR cc_start: 0.9052 (t80) cc_final: 0.8770 (t80) REVERT: X 17 LYS cc_start: 0.8887 (ttpt) cc_final: 0.8546 (ttmp) REVERT: X 38 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8690 (mm-30) REVERT: X 134 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8297 (pm20) REVERT: Y 87 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8804 (ttp80) REVERT: Y 145 TYR cc_start: 0.8907 (m-10) cc_final: 0.8521 (m-80) REVERT: Y 200 GLU cc_start: 0.8830 (pt0) cc_final: 0.8436 (pt0) REVERT: Z 131 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8158 (mmt) REVERT: Z 191 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7832 (m110) REVERT: Z 194 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8284 (mp) REVERT: Z 244 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8305 (mmtt) REVERT: Z 280 GLU cc_start: 0.8222 (pt0) cc_final: 0.7788 (pm20) REVERT: Z 281 LYS cc_start: 0.8751 (mttm) cc_final: 0.8422 (mtmt) REVERT: a 201 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8559 (ttpm) REVERT: a 242 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8166 (mm-30) REVERT: a 292 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8450 (tpp) REVERT: a 295 GLU cc_start: 0.8401 (mp0) cc_final: 0.8115 (mp0) REVERT: a 332 GLU cc_start: 0.8617 (pt0) cc_final: 0.8377 (pt0) REVERT: a 337 ARG cc_start: 0.8812 (mtt-85) cc_final: 0.8548 (mtm180) REVERT: b 77 ASP cc_start: 0.8564 (m-30) cc_final: 0.8269 (m-30) REVERT: b 115 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7763 (tm-30) REVERT: b 151 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: b 179 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8712 (mmt90) outliers start: 272 outliers final: 120 residues processed: 1185 average time/residue: 1.4078 time to fit residues: 2050.4561 Evaluate side-chains 1142 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 966 time to evaluate : 4.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 101 LYS Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 190 ARG Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 152 ARG Chi-restraints excluded: chain M residue 159 LEU Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 338 LYS Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 290 LYS Chi-restraints excluded: chain T residue 365 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 182 SER Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 140 MET Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 241 GLN Chi-restraints excluded: chain V residue 252 MET Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 201 LYS Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 87 ARG Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain Z residue 249 GLU Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 154 ASN Chi-restraints excluded: chain a residue 157 PHE Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 201 LYS Chi-restraints excluded: chain a residue 253 VAL Chi-restraints excluded: chain a residue 292 MET Chi-restraints excluded: chain a residue 293 THR Chi-restraints excluded: chain a residue 327 ASP Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 179 ARG Chi-restraints excluded: chain b residue 192 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 553 optimal weight: 5.9990 chunk 421 optimal weight: 8.9990 chunk 290 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 267 optimal weight: 1.9990 chunk 376 optimal weight: 0.7980 chunk 562 optimal weight: 0.0570 chunk 595 optimal weight: 9.9990 chunk 293 optimal weight: 0.6980 chunk 533 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 205 ASN D 18 GLN F 206 ASN F 305 GLN G 98 ASN G 147 GLN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 222 GLN L 291 GLN M 330 GLN O 228 ASN O 236 ASN P 205 ASN Q 257 HIS X 169 GLN Y 72 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN a 180 ASN b 94 GLN b 105 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 50122 Z= 0.259 Angle : 0.539 9.000 67810 Z= 0.289 Chirality : 0.043 0.173 7544 Planarity : 0.004 0.050 8790 Dihedral : 8.167 88.663 7202 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.69 % Favored : 98.19 % Rotamer: Outliers : 4.98 % Allowed : 20.35 % Favored : 74.67 % 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: 0.80 (0.10), residues: 6290 helix: 1.90 (0.10), residues: 2360 sheet: -0.23 (0.12), residues: 1600 loop : -0.24 (0.12), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 165 HIS 0.008 0.001 HIS D 187 PHE 0.017 0.002 PHE K 8 TYR 0.017 0.001 TYR Y 128 ARG 0.005 0.000 ARG O 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 990 time to evaluate : 4.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7857 (ptpt) REVERT: A 55 ASP cc_start: 0.8033 (m-30) cc_final: 0.7810 (m-30) REVERT: A 115 MET cc_start: 0.9165 (mmm) cc_final: 0.8960 (mmm) REVERT: A 125 GLN cc_start: 0.8111 (mt0) cc_final: 0.7665 (mm-40) REVERT: A 161 TRP cc_start: 0.8754 (t60) cc_final: 0.8302 (t-100) REVERT: A 184 ARG cc_start: 0.7939 (tpp80) cc_final: 0.7392 (mmm160) REVERT: A 215 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8117 (mmmt) REVERT: A 217 LYS cc_start: 0.8687 (tttt) cc_final: 0.8056 (pttp) REVERT: B 3 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.5985 (tt0) REVERT: B 118 GLU cc_start: 0.8441 (tt0) cc_final: 0.8103 (tt0) REVERT: B 175 ARG cc_start: 0.8244 (mmm160) cc_final: 0.8036 (mmm160) REVERT: B 184 ASP cc_start: 0.7705 (t0) cc_final: 0.7435 (m-30) REVERT: C 40 LYS cc_start: 0.8487 (mmtp) cc_final: 0.7947 (pttt) REVERT: C 130 TYR cc_start: 0.8518 (m-80) cc_final: 0.8276 (m-80) REVERT: C 237 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8277 (tppt) REVERT: C 265 ARG cc_start: 0.7732 (tpp-160) cc_final: 0.7510 (tpt-90) REVERT: D 4 ASP cc_start: 0.8346 (p0) cc_final: 0.8067 (p0) REVERT: D 52 LYS cc_start: 0.7937 (mttp) cc_final: 0.7530 (mppt) REVERT: D 57 ARG cc_start: 0.7762 (tmm160) cc_final: 0.7288 (ptt90) REVERT: D 61 LYS cc_start: 0.8827 (mptp) cc_final: 0.8527 (mmpt) REVERT: D 174 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8310 (mtpt) REVERT: D 177 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8052 (mmtp) REVERT: D 180 MET cc_start: 0.8253 (mtt) cc_final: 0.7882 (mtm) REVERT: D 215 ARG cc_start: 0.8470 (ttp-170) cc_final: 0.8018 (mtp-110) REVERT: D 221 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7117 (tp30) REVERT: D 232 GLU cc_start: 0.7234 (tt0) cc_final: 0.6803 (mt-10) REVERT: E 140 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8579 (mm) REVERT: E 190 GLU cc_start: 0.8460 (tp30) cc_final: 0.8148 (tp30) REVERT: E 278 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7502 (mt0) REVERT: E 283 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7045 (tm-30) REVERT: E 300 ASP cc_start: 0.7974 (m-30) cc_final: 0.7444 (m-30) REVERT: E 326 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8446 (mmtm) REVERT: E 328 HIS cc_start: 0.8482 (m-70) cc_final: 0.8280 (m90) REVERT: E 342 MET cc_start: 0.6497 (ttm) cc_final: 0.6073 (ttm) REVERT: F 220 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6941 (tp30) REVERT: F 221 LEU cc_start: 0.7854 (tt) cc_final: 0.7587 (tm) REVERT: F 270 MET cc_start: 0.8992 (mmm) cc_final: 0.8628 (mmm) REVERT: F 402 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6802 (mmmt) REVERT: G 43 LYS cc_start: 0.8659 (mmtp) cc_final: 0.8418 (mmmt) REVERT: G 51 GLU cc_start: 0.8265 (tt0) cc_final: 0.7718 (pp20) REVERT: G 115 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8253 (mpt-90) REVERT: G 182 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8338 (p) REVERT: G 184 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7578 (pt) REVERT: H 123 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8511 (p0) REVERT: H 139 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8352 (ttpp) REVERT: H 201 MET cc_start: 0.8875 (mtt) cc_final: 0.8613 (mtt) REVERT: H 279 MET cc_start: 0.8959 (mtm) cc_final: 0.8559 (mtp) REVERT: I 120 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8672 (mm110) REVERT: I 225 MET cc_start: 0.7371 (mtp) cc_final: 0.6969 (mtt) REVERT: I 226 TYR cc_start: 0.7147 (t80) cc_final: 0.6476 (t80) REVERT: I 230 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: J 4 MET cc_start: 0.9154 (mmm) cc_final: 0.8860 (mmt) REVERT: J 38 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8564 (mm-30) REVERT: J 48 SER cc_start: 0.9146 (p) cc_final: 0.8936 (m) REVERT: J 75 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8634 (mmtt) REVERT: J 97 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8153 (mt-10) REVERT: J 114 LYS cc_start: 0.7997 (tttt) cc_final: 0.7522 (tppt) REVERT: K 1 MET cc_start: 0.7539 (mmm) cc_final: 0.7081 (mmm) REVERT: K 50 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: K 196 LYS cc_start: 0.8742 (ptmm) cc_final: 0.8497 (ptmt) REVERT: K 200 GLU cc_start: 0.8954 (pt0) cc_final: 0.8582 (pt0) REVERT: K 206 HIS cc_start: 0.8273 (p90) cc_final: 0.7993 (p-80) REVERT: L 155 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8221 (mp0) REVERT: L 191 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7788 (m110) REVERT: M 174 TYR cc_start: 0.8773 (m-10) cc_final: 0.8032 (m-10) REVERT: M 212 LYS cc_start: 0.9025 (tttm) cc_final: 0.8755 (ttpp) REVERT: M 226 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7273 (ptp-170) REVERT: M 281 ARG cc_start: 0.8403 (mtp85) cc_final: 0.7635 (mtp-110) REVERT: M 332 GLU cc_start: 0.8341 (pt0) cc_final: 0.8121 (pt0) REVERT: M 338 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8277 (mmtm) REVERT: N 69 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8163 (mtt90) REVERT: N 100 ASP cc_start: 0.8093 (t70) cc_final: 0.7827 (t0) REVERT: N 106 MET cc_start: 0.8867 (mpt) cc_final: 0.8195 (mpt) REVERT: N 148 GLN cc_start: 0.8978 (tt0) cc_final: 0.8665 (tt0) REVERT: N 179 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8599 (mtt-85) REVERT: N 203 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: O 7 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7298 (p0) REVERT: O 36 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8733 (t) REVERT: O 67 TYR cc_start: 0.9081 (m-80) cc_final: 0.8761 (m-80) REVERT: O 93 GLU cc_start: 0.8168 (tt0) cc_final: 0.7949 (tm-30) REVERT: O 115 MET cc_start: 0.9227 (mmm) cc_final: 0.8945 (mmp) REVERT: O 125 GLN cc_start: 0.8306 (mt0) cc_final: 0.8094 (tt0) REVERT: O 186 LYS cc_start: 0.8490 (mttt) cc_final: 0.8248 (mttt) REVERT: O 190 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8383 (mp) REVERT: O 217 LYS cc_start: 0.8419 (tttt) cc_final: 0.8207 (pttp) REVERT: O 240 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8003 (mm-30) REVERT: P 16 LYS cc_start: 0.8894 (ptmt) cc_final: 0.8129 (mmtt) REVERT: P 85 ILE cc_start: 0.9211 (mt) cc_final: 0.8929 (mt) REVERT: P 154 TRP cc_start: 0.7931 (m100) cc_final: 0.6923 (m-90) REVERT: P 202 THR cc_start: 0.8987 (p) cc_final: 0.8586 (t) REVERT: P 226 ASP cc_start: 0.7912 (m-30) cc_final: 0.7665 (t70) REVERT: Q 15 GLU cc_start: 0.8160 (tt0) cc_final: 0.7936 (tp30) REVERT: Q 29 GLN cc_start: 0.8184 (mt0) cc_final: 0.7959 (mt0) REVERT: Q 53 HIS cc_start: 0.8722 (t-90) cc_final: 0.8311 (t-90) REVERT: Q 59 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8276 (pt0) REVERT: Q 193 ASP cc_start: 0.8448 (t0) cc_final: 0.8182 (m-30) REVERT: Q 204 LYS cc_start: 0.8640 (tttt) cc_final: 0.8223 (tptp) REVERT: R 23 GLN cc_start: 0.8185 (mt0) cc_final: 0.7860 (mm-40) REVERT: R 49 SER cc_start: 0.6294 (t) cc_final: 0.5810 (p) REVERT: R 54 GLN cc_start: 0.8226 (pt0) cc_final: 0.7537 (mm110) REVERT: R 60 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7846 (mpt90) REVERT: R 141 LYS cc_start: 0.8190 (tptt) cc_final: 0.7884 (tppp) REVERT: R 213 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7903 (mp0) REVERT: R 219 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: S 118 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8434 (mp0) REVERT: S 249 LYS cc_start: 0.8667 (mmtm) cc_final: 0.8251 (mmmt) REVERT: S 336 LYS cc_start: 0.8040 (tttt) cc_final: 0.7590 (tppp) REVERT: T 169 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7725 (pm20) REVERT: T 190 ASN cc_start: 0.8022 (OUTLIER) cc_final: 0.7720 (m-40) REVERT: T 290 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8403 (mttt) REVERT: T 343 HIS cc_start: 0.7333 (m90) cc_final: 0.6995 (m-70) REVERT: T 347 CYS cc_start: 0.8736 (m) cc_final: 0.8390 (m) REVERT: T 404 ARG cc_start: 0.5510 (OUTLIER) cc_final: 0.5124 (ppt170) REVERT: U 86 ARG cc_start: 0.8727 (mtp180) cc_final: 0.8506 (mmm-85) REVERT: U 94 GLN cc_start: 0.8521 (tt0) cc_final: 0.8286 (tm-30) REVERT: U 115 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8281 (mmt90) REVERT: U 203 LYS cc_start: 0.7947 (mttt) cc_final: 0.7442 (mtmm) REVERT: V 93 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8493 (tttm) REVERT: V 105 ASP cc_start: 0.8673 (m-30) cc_final: 0.8422 (m-30) REVERT: V 143 MET cc_start: 0.8502 (ttp) cc_final: 0.8153 (mmp) REVERT: V 201 MET cc_start: 0.8806 (mtt) cc_final: 0.8539 (mtm) REVERT: V 273 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8195 (tppt) REVERT: W 61 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7507 (mmt90) REVERT: W 82 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: W 118 ARG cc_start: 0.8832 (ttp80) cc_final: 0.8423 (ttm110) REVERT: W 119 TYR cc_start: 0.8957 (m-80) cc_final: 0.8667 (m-80) REVERT: W 149 ASP cc_start: 0.8152 (m-30) cc_final: 0.7723 (m-30) REVERT: X 6 TYR cc_start: 0.9064 (t80) cc_final: 0.8761 (t80) REVERT: X 14 MET cc_start: 0.8775 (mtt) cc_final: 0.8520 (mtt) REVERT: X 17 LYS cc_start: 0.8894 (ttpt) cc_final: 0.8589 (ttmm) REVERT: X 38 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8696 (mm-30) REVERT: X 94 MET cc_start: 0.9241 (mtp) cc_final: 0.8727 (mtp) REVERT: X 134 GLU cc_start: 0.8569 (pt0) cc_final: 0.8240 (pm20) REVERT: X 192 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8870 (mtmm) REVERT: Y 38 GLN cc_start: 0.9176 (tt0) cc_final: 0.8959 (tt0) REVERT: Y 87 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8812 (ttp80) REVERT: Y 145 TYR cc_start: 0.8908 (m-10) cc_final: 0.8576 (m-80) REVERT: Y 200 GLU cc_start: 0.8820 (pt0) cc_final: 0.8375 (pt0) REVERT: Z 131 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8165 (mmt) REVERT: Z 190 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8697 (ptt-90) REVERT: Z 191 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7865 (m110) REVERT: Z 194 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8273 (mp) REVERT: Z 244 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8294 (mmtt) REVERT: Z 280 GLU cc_start: 0.8266 (pt0) cc_final: 0.7797 (pm20) REVERT: Z 281 LYS cc_start: 0.8729 (mttm) cc_final: 0.8383 (mtmt) REVERT: a 201 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8578 (ttpm) REVERT: a 242 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8154 (mm-30) REVERT: a 295 GLU cc_start: 0.8457 (mp0) cc_final: 0.8047 (mp0) REVERT: a 332 GLU cc_start: 0.8561 (pt0) cc_final: 0.8336 (pt0) REVERT: b 77 ASP cc_start: 0.8537 (m-30) cc_final: 0.8271 (m-30) REVERT: b 115 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7848 (tm-30) REVERT: b 151 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8163 (mm-30) REVERT: b 179 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8603 (mmt90) outliers start: 261 outliers final: 116 residues processed: 1153 average time/residue: 1.4284 time to fit residues: 2022.1554 Evaluate side-chains 1127 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 961 time to evaluate : 4.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 402 LYS Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain J residue 12 MET Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 159 LEU Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain M residue 338 LYS Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 172 GLN Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 300 ASP Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 290 LYS Chi-restraints excluded: chain T residue 365 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 182 SER Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 227 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 93 LYS Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 252 MET Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 192 LYS Chi-restraints excluded: chain X residue 201 LYS Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 87 ARG Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 154 ASN Chi-restraints excluded: chain a residue 201 LYS Chi-restraints excluded: chain a residue 253 VAL Chi-restraints excluded: chain a residue 327 ASP Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 179 ARG Chi-restraints excluded: chain b residue 192 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 495 optimal weight: 0.0000 chunk 337 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 443 optimal weight: 6.9990 chunk 245 optimal weight: 4.9990 chunk 508 optimal weight: 0.8980 chunk 411 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 304 optimal weight: 4.9990 chunk 534 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 205 ASN D 18 GLN E 191 HIS F 206 ASN F 305 GLN F 371 ASN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 GLN L 222 GLN L 291 GLN M 130 GLN O 228 ASN O 236 ASN P 205 ASN U 64 ASN V 241 GLN W 229 GLN Y 22 ASN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN a 130 GLN b 94 GLN b 105 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 50122 Z= 0.220 Angle : 0.522 8.765 67810 Z= 0.279 Chirality : 0.042 0.168 7544 Planarity : 0.004 0.049 8790 Dihedral : 7.607 88.274 7168 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.84 % Favored : 98.06 % Rotamer: Outliers : 4.94 % Allowed : 20.73 % Favored : 74.32 % 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: 0.96 (0.10), residues: 6290 helix: 2.06 (0.10), residues: 2358 sheet: -0.11 (0.12), residues: 1574 loop : -0.19 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 154 HIS 0.008 0.001 HIS D 187 PHE 0.016 0.001 PHE K 8 TYR 0.018 0.001 TYR J 96 ARG 0.010 0.000 ARG N 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1282 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1023 time to evaluate : 4.176 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7813 (ptpt) REVERT: A 125 GLN cc_start: 0.8052 (mt0) cc_final: 0.7621 (mm-40) REVERT: A 161 TRP cc_start: 0.8756 (t60) cc_final: 0.8238 (t-100) REVERT: A 184 ARG cc_start: 0.7937 (tpp80) cc_final: 0.7405 (mmm160) REVERT: A 215 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8147 (mmtt) REVERT: A 217 LYS cc_start: 0.8653 (tttt) cc_final: 0.8063 (pttt) REVERT: B 3 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6066 (tt0) REVERT: B 118 GLU cc_start: 0.8439 (tt0) cc_final: 0.8111 (tt0) REVERT: C 40 LYS cc_start: 0.8555 (mmtp) cc_final: 0.7977 (pttt) REVERT: C 130 TYR cc_start: 0.8445 (m-80) cc_final: 0.8239 (m-80) REVERT: C 237 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8179 (tppt) REVERT: C 265 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7497 (tpt-90) REVERT: C 266 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6935 (pt0) REVERT: D 4 ASP cc_start: 0.8273 (p0) cc_final: 0.8060 (p0) REVERT: D 18 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.7285 (mp-120) REVERT: D 52 LYS cc_start: 0.7964 (mttp) cc_final: 0.7516 (mppt) REVERT: D 57 ARG cc_start: 0.7679 (tmm160) cc_final: 0.7160 (ptt90) REVERT: D 61 LYS cc_start: 0.8788 (mptp) cc_final: 0.8480 (mmpt) REVERT: D 166 GLN cc_start: 0.7904 (tp40) cc_final: 0.7616 (tp40) REVERT: D 174 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8336 (mtpt) REVERT: D 177 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7958 (mmtp) REVERT: D 180 MET cc_start: 0.8261 (mtt) cc_final: 0.7822 (mtm) REVERT: D 215 ARG cc_start: 0.8470 (ttp-170) cc_final: 0.8012 (mtp-110) REVERT: D 221 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7125 (tp30) REVERT: D 232 GLU cc_start: 0.7232 (tt0) cc_final: 0.6819 (mt-10) REVERT: E 140 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8579 (mm) REVERT: E 190 GLU cc_start: 0.8456 (tp30) cc_final: 0.8122 (tp30) REVERT: E 278 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7475 (mt0) REVERT: E 300 ASP cc_start: 0.7966 (m-30) cc_final: 0.7405 (m-30) REVERT: E 329 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8533 (mtt) REVERT: E 342 MET cc_start: 0.6530 (ttm) cc_final: 0.6045 (ttm) REVERT: F 221 LEU cc_start: 0.7781 (tt) cc_final: 0.7559 (tm) REVERT: F 270 MET cc_start: 0.8940 (mmm) cc_final: 0.8569 (mmm) REVERT: F 402 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6849 (mmmt) REVERT: G 13 ASP cc_start: 0.8809 (p0) cc_final: 0.8577 (p0) REVERT: G 43 LYS cc_start: 0.8630 (mmtp) cc_final: 0.8355 (mmmt) REVERT: G 51 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7717 (pp20) REVERT: G 115 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8272 (mpt-90) REVERT: G 182 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8339 (p) REVERT: G 184 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7573 (pt) REVERT: H 123 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8510 (p0) REVERT: H 139 LYS cc_start: 0.8745 (ttmm) cc_final: 0.8323 (ttpp) REVERT: H 140 MET cc_start: 0.8870 (mmm) cc_final: 0.8491 (mpt) REVERT: H 201 MET cc_start: 0.8867 (mtt) cc_final: 0.8493 (mtp) REVERT: H 279 MET cc_start: 0.8917 (mtm) cc_final: 0.8513 (mtp) REVERT: I 120 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8321 (mp10) REVERT: I 225 MET cc_start: 0.7381 (mtp) cc_final: 0.6993 (mtt) REVERT: I 226 TYR cc_start: 0.7180 (t80) cc_final: 0.6525 (t80) REVERT: I 230 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: J 4 MET cc_start: 0.9126 (mmm) cc_final: 0.8858 (mmt) REVERT: J 38 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8555 (mm-30) REVERT: J 75 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8626 (mmtt) REVERT: J 97 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8155 (mt-10) REVERT: J 114 LYS cc_start: 0.8039 (tttt) cc_final: 0.7607 (mmtm) REVERT: J 134 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7599 (pp20) REVERT: K 1 MET cc_start: 0.7551 (mmm) cc_final: 0.7107 (mmm) REVERT: K 181 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8581 (mpt180) REVERT: K 196 LYS cc_start: 0.8716 (ptmm) cc_final: 0.8471 (ptmt) REVERT: K 200 GLU cc_start: 0.8906 (pt0) cc_final: 0.8551 (pt0) REVERT: K 206 HIS cc_start: 0.8273 (p90) cc_final: 0.8006 (p-80) REVERT: L 134 LEU cc_start: 0.9085 (tt) cc_final: 0.8463 (mp) REVERT: L 155 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: L 191 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7884 (m110) REVERT: M 174 TYR cc_start: 0.8799 (m-10) cc_final: 0.8046 (m-10) REVERT: M 186 ARG cc_start: 0.9331 (OUTLIER) cc_final: 0.7906 (ttm110) REVERT: M 226 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7260 (ptp-170) REVERT: M 332 GLU cc_start: 0.8306 (pt0) cc_final: 0.8075 (pt0) REVERT: N 69 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8195 (mtt90) REVERT: N 100 ASP cc_start: 0.8071 (t70) cc_final: 0.7811 (t0) REVERT: N 106 MET cc_start: 0.8817 (mpt) cc_final: 0.8083 (mpt) REVERT: N 148 GLN cc_start: 0.8904 (tt0) cc_final: 0.8595 (tt0) REVERT: N 179 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8641 (mtt90) REVERT: N 183 LYS cc_start: 0.8927 (ttpt) cc_final: 0.8690 (tppp) REVERT: N 195 ARG cc_start: 0.8694 (mtp-110) cc_final: 0.8302 (mtp85) REVERT: N 203 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: O 6 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.7192 (t80) REVERT: O 7 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7269 (p0) REVERT: O 67 TYR cc_start: 0.9051 (m-80) cc_final: 0.8718 (m-80) REVERT: O 93 GLU cc_start: 0.8117 (tt0) cc_final: 0.7470 (tm-30) REVERT: O 97 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: O 115 MET cc_start: 0.9230 (mmm) cc_final: 0.8957 (mmp) REVERT: O 125 GLN cc_start: 0.8278 (mt0) cc_final: 0.8076 (tt0) REVERT: O 178 MET cc_start: 0.9172 (mmp) cc_final: 0.8886 (tpt) REVERT: O 186 LYS cc_start: 0.8443 (mttt) cc_final: 0.8224 (mttt) REVERT: O 190 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8363 (mp) REVERT: O 240 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8051 (mm-30) REVERT: P 16 LYS cc_start: 0.8837 (ptmt) cc_final: 0.8107 (mmtm) REVERT: P 85 ILE cc_start: 0.9203 (mt) cc_final: 0.8906 (mt) REVERT: P 202 THR cc_start: 0.8954 (p) cc_final: 0.8553 (t) REVERT: P 226 ASP cc_start: 0.7920 (m-30) cc_final: 0.7691 (t70) REVERT: Q 15 GLU cc_start: 0.8257 (tt0) cc_final: 0.7999 (tp30) REVERT: Q 53 HIS cc_start: 0.8744 (t-90) cc_final: 0.8311 (t-90) REVERT: Q 59 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: Q 193 ASP cc_start: 0.8438 (t0) cc_final: 0.8172 (m-30) REVERT: Q 204 LYS cc_start: 0.8611 (tttt) cc_final: 0.8249 (tptp) REVERT: Q 266 GLU cc_start: 0.6862 (tm-30) cc_final: 0.6649 (tm-30) REVERT: R 23 GLN cc_start: 0.8173 (mt0) cc_final: 0.7864 (mm-40) REVERT: R 49 SER cc_start: 0.6285 (t) cc_final: 0.5809 (p) REVERT: R 54 GLN cc_start: 0.8152 (pt0) cc_final: 0.7535 (mm110) REVERT: R 213 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7883 (mp0) REVERT: R 219 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: S 118 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8441 (mp0) REVERT: S 249 LYS cc_start: 0.8662 (mmtm) cc_final: 0.8343 (mmmt) REVERT: S 336 LYS cc_start: 0.7999 (tttt) cc_final: 0.7566 (tppp) REVERT: T 270 MET cc_start: 0.8768 (mmm) cc_final: 0.8477 (mmm) REVERT: T 290 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8485 (mttt) REVERT: T 343 HIS cc_start: 0.7296 (m90) cc_final: 0.6939 (m-70) REVERT: T 347 CYS cc_start: 0.8732 (m) cc_final: 0.8369 (m) REVERT: T 404 ARG cc_start: 0.5580 (OUTLIER) cc_final: 0.5153 (ppt170) REVERT: U 94 GLN cc_start: 0.8506 (tt0) cc_final: 0.8287 (tm-30) REVERT: U 115 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8437 (mmt90) REVERT: U 188 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8379 (pt0) REVERT: U 203 LYS cc_start: 0.7936 (mttt) cc_final: 0.7455 (mtmm) REVERT: V 143 MET cc_start: 0.8495 (ttp) cc_final: 0.8168 (mmp) REVERT: V 201 MET cc_start: 0.8784 (mtt) cc_final: 0.8524 (mtm) REVERT: V 273 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8194 (tppt) REVERT: W 61 ARG cc_start: 0.7710 (mtp85) cc_final: 0.7454 (mmt90) REVERT: W 82 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8432 (tt0) REVERT: W 87 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8327 (ptm) REVERT: W 106 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8832 (tt) REVERT: W 118 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8420 (ttm110) REVERT: W 119 TYR cc_start: 0.8919 (m-80) cc_final: 0.8689 (m-80) REVERT: W 149 ASP cc_start: 0.8170 (m-30) cc_final: 0.7836 (m-30) REVERT: X 6 TYR cc_start: 0.9043 (t80) cc_final: 0.8760 (t80) REVERT: X 14 MET cc_start: 0.8777 (mtt) cc_final: 0.8545 (mtt) REVERT: X 17 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8565 (ttmm) REVERT: X 38 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8701 (mm-30) REVERT: X 78 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: X 134 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8189 (pm20) REVERT: X 191 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8332 (p) REVERT: Y 38 GLN cc_start: 0.9149 (tt0) cc_final: 0.8943 (tt0) REVERT: Y 145 TYR cc_start: 0.8885 (m-10) cc_final: 0.8546 (m-80) REVERT: Y 200 GLU cc_start: 0.8881 (pt0) cc_final: 0.8438 (pt0) REVERT: Z 131 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8150 (mmt) REVERT: Z 191 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7798 (m110) REVERT: Z 194 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8236 (mp) REVERT: Z 244 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8366 (mmtt) REVERT: Z 280 GLU cc_start: 0.8224 (pt0) cc_final: 0.7799 (mp0) REVERT: Z 281 LYS cc_start: 0.8720 (mttm) cc_final: 0.8382 (mtmt) REVERT: a 198 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8511 (mttt) REVERT: a 242 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8162 (mm-30) REVERT: a 295 GLU cc_start: 0.8356 (mp0) cc_final: 0.7961 (mp0) REVERT: b 77 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8358 (m-30) REVERT: b 106 MET cc_start: 0.8866 (mtt) cc_final: 0.8304 (mtt) REVERT: b 115 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7890 (tm-30) REVERT: b 151 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8188 (mm-30) REVERT: b 179 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8588 (mpt180) outliers start: 259 outliers final: 118 residues processed: 1180 average time/residue: 1.3900 time to fit residues: 2021.4434 Evaluate side-chains 1137 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 966 time to evaluate : 4.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 402 LYS Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain J residue 12 MET Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 159 LEU Chi-restraints excluded: chain M residue 186 ARG Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 260 LEU Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 152 LYS Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 6 PHE Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 97 ASP Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 220 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 268 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 290 LYS Chi-restraints excluded: chain T residue 365 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 182 SER Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 188 GLU Chi-restraints excluded: chain U residue 227 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 252 MET Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain X residue 201 LYS Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 198 LYS Chi-restraints excluded: chain a residue 253 VAL Chi-restraints excluded: chain a residue 327 ASP Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 179 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 200 optimal weight: 2.9990 chunk 536 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 349 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 596 optimal weight: 1.9990 chunk 494 optimal weight: 5.9990 chunk 275 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 312 optimal weight: 0.0010 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 205 ASN D 18 GLN D 187 HIS F 206 ASN F 305 GLN G 147 GLN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 222 GLN ** L 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN M 234 ASN O 228 ASN O 236 ASN P 205 ASN Q 186 HIS T 305 GLN V 241 GLN W 229 GLN X 65 ASN Y 72 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN b 75 ASN b 94 GLN b 105 GLN b 148 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 50122 Z= 0.247 Angle : 0.533 8.683 67810 Z= 0.283 Chirality : 0.043 0.206 7544 Planarity : 0.004 0.050 8790 Dihedral : 7.393 88.555 7143 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.78 % Favored : 98.14 % Rotamer: Outliers : 4.81 % Allowed : 21.29 % Favored : 73.90 % 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: 1.02 (0.10), residues: 6290 helix: 2.10 (0.10), residues: 2358 sheet: -0.07 (0.12), residues: 1572 loop : -0.16 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 165 HIS 0.007 0.001 HIS D 187 PHE 0.018 0.001 PHE K 8 TYR 0.022 0.001 TYR J 96 ARG 0.008 0.000 ARG N 159 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 995 time to evaluate : 4.269 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7818 (ptpt) REVERT: A 125 GLN cc_start: 0.8056 (mt0) cc_final: 0.7629 (mm-40) REVERT: A 161 TRP cc_start: 0.8705 (t60) cc_final: 0.8201 (t-100) REVERT: A 184 ARG cc_start: 0.7939 (tpp80) cc_final: 0.7409 (mmm160) REVERT: A 215 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8115 (mmmt) REVERT: A 217 LYS cc_start: 0.8676 (tttt) cc_final: 0.8077 (pttt) REVERT: B 3 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6492 (tt0) REVERT: B 118 GLU cc_start: 0.8441 (tt0) cc_final: 0.8100 (tt0) REVERT: C 40 LYS cc_start: 0.8577 (mmtp) cc_final: 0.7988 (pttt) REVERT: C 66 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8556 (t) REVERT: C 187 GLU cc_start: 0.7676 (pm20) cc_final: 0.7449 (mp0) REVERT: C 237 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8250 (tppt) REVERT: C 262 ASP cc_start: 0.7287 (t0) cc_final: 0.7028 (t0) REVERT: C 265 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7469 (tpt-90) REVERT: C 266 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6935 (pt0) REVERT: D 4 ASP cc_start: 0.8220 (p0) cc_final: 0.7951 (p0) REVERT: D 52 LYS cc_start: 0.8006 (mttp) cc_final: 0.7541 (mppt) REVERT: D 57 ARG cc_start: 0.7682 (tmm160) cc_final: 0.7155 (ptt90) REVERT: D 166 GLN cc_start: 0.7898 (tp40) cc_final: 0.7636 (tp40) REVERT: D 174 LYS cc_start: 0.8554 (mtmt) cc_final: 0.8329 (mtpt) REVERT: D 177 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7954 (mmtp) REVERT: D 180 MET cc_start: 0.8268 (mtt) cc_final: 0.7836 (mtm) REVERT: D 215 ARG cc_start: 0.8470 (ttp-170) cc_final: 0.8015 (mtp-110) REVERT: D 221 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7112 (tp30) REVERT: D 232 GLU cc_start: 0.7300 (tt0) cc_final: 0.6860 (mt-10) REVERT: E 107 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.5813 (mp0) REVERT: E 140 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8588 (mm) REVERT: E 190 GLU cc_start: 0.8446 (tp30) cc_final: 0.8150 (tp30) REVERT: E 278 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7465 (mt0) REVERT: E 300 ASP cc_start: 0.7987 (m-30) cc_final: 0.7407 (m-30) REVERT: E 329 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8591 (mtt) REVERT: E 342 MET cc_start: 0.6408 (ttm) cc_final: 0.5896 (ttm) REVERT: F 221 LEU cc_start: 0.7767 (tt) cc_final: 0.7540 (tm) REVERT: F 270 MET cc_start: 0.8962 (mmm) cc_final: 0.8592 (mmm) REVERT: F 369 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7399 (mm-30) REVERT: F 402 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6746 (tptp) REVERT: G 13 ASP cc_start: 0.8835 (p0) cc_final: 0.8626 (p0) REVERT: G 43 LYS cc_start: 0.8688 (mmtp) cc_final: 0.8419 (mmmt) REVERT: G 51 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: G 115 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8185 (mpt-90) REVERT: G 184 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7615 (pt) REVERT: H 123 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8584 (p0) REVERT: H 139 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8212 (ttpp) REVERT: H 143 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8058 (mpm) REVERT: H 201 MET cc_start: 0.8865 (mtt) cc_final: 0.8602 (mtt) REVERT: H 279 MET cc_start: 0.8910 (mtm) cc_final: 0.8482 (mtp) REVERT: I 59 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.7987 (mtm-85) REVERT: I 120 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8332 (mt0) REVERT: I 225 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6768 (mtt) REVERT: I 226 TYR cc_start: 0.7182 (t80) cc_final: 0.6542 (t80) REVERT: J 4 MET cc_start: 0.9123 (mmm) cc_final: 0.8853 (mmt) REVERT: J 38 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8566 (mm-30) REVERT: J 75 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8648 (mmtt) REVERT: J 97 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8150 (mt-10) REVERT: J 114 LYS cc_start: 0.8030 (tttt) cc_final: 0.7610 (mmtm) REVERT: J 134 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7589 (pp20) REVERT: K 1 MET cc_start: 0.7556 (mmm) cc_final: 0.7117 (mmm) REVERT: K 77 SER cc_start: 0.8853 (p) cc_final: 0.8637 (p) REVERT: K 129 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8334 (mtp) REVERT: K 181 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8541 (mpt180) REVERT: K 196 LYS cc_start: 0.8714 (ptmm) cc_final: 0.8473 (ptmt) REVERT: K 200 GLU cc_start: 0.8887 (pt0) cc_final: 0.8532 (pt0) REVERT: K 206 HIS cc_start: 0.8274 (p90) cc_final: 0.8005 (p-80) REVERT: L 134 LEU cc_start: 0.9087 (tt) cc_final: 0.8466 (mp) REVERT: L 155 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: L 191 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7899 (m110) REVERT: M 174 TYR cc_start: 0.8833 (m-10) cc_final: 0.8141 (m-10) REVERT: M 186 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.8090 (ttm110) REVERT: M 226 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7239 (ptp-170) REVERT: M 332 GLU cc_start: 0.8310 (pt0) cc_final: 0.8094 (pt0) REVERT: M 338 LYS cc_start: 0.8524 (tppt) cc_final: 0.8037 (mmtp) REVERT: N 69 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8177 (mtt90) REVERT: N 106 MET cc_start: 0.8797 (mpt) cc_final: 0.8099 (mpt) REVERT: N 148 GLN cc_start: 0.8901 (tt0) cc_final: 0.8593 (tt0) REVERT: N 179 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8619 (mtt90) REVERT: N 183 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8686 (tppp) REVERT: N 195 ARG cc_start: 0.8696 (mtp-110) cc_final: 0.8305 (mtp85) REVERT: N 203 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: O 6 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.7216 (t80) REVERT: O 7 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7285 (p0) REVERT: O 67 TYR cc_start: 0.9041 (m-80) cc_final: 0.8750 (m-80) REVERT: O 93 GLU cc_start: 0.8181 (tt0) cc_final: 0.7627 (tm-30) REVERT: O 97 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: O 115 MET cc_start: 0.9239 (mmm) cc_final: 0.8970 (mmp) REVERT: O 125 GLN cc_start: 0.8281 (mt0) cc_final: 0.8080 (tt0) REVERT: O 178 MET cc_start: 0.9171 (mmp) cc_final: 0.8939 (tpt) REVERT: O 186 LYS cc_start: 0.8463 (mttt) cc_final: 0.8258 (mttt) REVERT: O 190 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8380 (mp) REVERT: O 240 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8003 (mm-30) REVERT: P 16 LYS cc_start: 0.8877 (ptmt) cc_final: 0.8108 (mmtm) REVERT: P 202 THR cc_start: 0.9003 (p) cc_final: 0.8591 (t) REVERT: P 226 ASP cc_start: 0.7926 (m-30) cc_final: 0.7712 (t70) REVERT: Q 15 GLU cc_start: 0.8264 (tt0) cc_final: 0.8008 (tp30) REVERT: Q 53 HIS cc_start: 0.8750 (t-90) cc_final: 0.8343 (t-90) REVERT: Q 59 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8313 (pt0) REVERT: Q 193 ASP cc_start: 0.8444 (t0) cc_final: 0.8184 (m-30) REVERT: Q 204 LYS cc_start: 0.8645 (tttt) cc_final: 0.8282 (tptp) REVERT: Q 266 GLU cc_start: 0.6922 (tm-30) cc_final: 0.6707 (tm-30) REVERT: R 23 GLN cc_start: 0.8178 (mt0) cc_final: 0.7862 (mm-40) REVERT: R 54 GLN cc_start: 0.8119 (pt0) cc_final: 0.7512 (mm110) REVERT: R 174 LYS cc_start: 0.7904 (mmtp) cc_final: 0.7523 (mtmm) REVERT: R 213 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7804 (mp0) REVERT: S 137 SER cc_start: 0.8732 (m) cc_final: 0.8518 (p) REVERT: S 249 LYS cc_start: 0.8703 (mmtm) cc_final: 0.8348 (mmmt) REVERT: S 336 LYS cc_start: 0.8003 (tttt) cc_final: 0.7573 (tppp) REVERT: T 190 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7737 (m-40) REVERT: T 343 HIS cc_start: 0.7249 (m90) cc_final: 0.6885 (m-70) REVERT: T 347 CYS cc_start: 0.8735 (m) cc_final: 0.8354 (m) REVERT: T 404 ARG cc_start: 0.5655 (OUTLIER) cc_final: 0.5170 (ppt170) REVERT: U 29 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8213 (mtmt) REVERT: U 94 GLN cc_start: 0.8564 (tt0) cc_final: 0.8341 (tm-30) REVERT: U 115 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8441 (mmt90) REVERT: U 188 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8367 (pt0) REVERT: V 143 MET cc_start: 0.8500 (ttp) cc_final: 0.8170 (mmp) REVERT: V 201 MET cc_start: 0.8796 (mtt) cc_final: 0.8531 (mtm) REVERT: V 273 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8177 (tppt) REVERT: W 61 ARG cc_start: 0.7711 (mtp85) cc_final: 0.7476 (mmt90) REVERT: W 82 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: W 106 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8894 (tt) REVERT: W 118 ARG cc_start: 0.8825 (ttp80) cc_final: 0.8415 (ttm110) REVERT: W 119 TYR cc_start: 0.8927 (m-80) cc_final: 0.8671 (m-80) REVERT: W 149 ASP cc_start: 0.8078 (m-30) cc_final: 0.7759 (m-30) REVERT: X 6 TYR cc_start: 0.9041 (t80) cc_final: 0.8794 (t80) REVERT: X 14 MET cc_start: 0.8786 (mtt) cc_final: 0.8543 (mtt) REVERT: X 38 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8704 (mm-30) REVERT: X 78 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: X 134 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8176 (pm20) REVERT: X 191 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8360 (p) REVERT: Y 38 GLN cc_start: 0.9150 (tt0) cc_final: 0.8947 (tt0) REVERT: Y 129 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8608 (mtm) REVERT: Y 145 TYR cc_start: 0.8896 (m-10) cc_final: 0.8618 (m-80) REVERT: Y 200 GLU cc_start: 0.8865 (pt0) cc_final: 0.8421 (pt0) REVERT: Z 131 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8128 (mmt) REVERT: Z 191 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7771 (m110) REVERT: Z 196 MET cc_start: 0.8962 (ptp) cc_final: 0.8698 (ptm) REVERT: Z 244 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8378 (mmtt) REVERT: Z 249 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8426 (mm-30) REVERT: Z 280 GLU cc_start: 0.8241 (pt0) cc_final: 0.7817 (mp0) REVERT: Z 281 LYS cc_start: 0.8683 (mttm) cc_final: 0.8333 (mtmt) REVERT: Z 287 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8527 (p) REVERT: a 198 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8478 (mttt) REVERT: a 242 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8172 (mm-30) REVERT: a 295 GLU cc_start: 0.8377 (mp0) cc_final: 0.8013 (mp0) REVERT: b 68 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8410 (tp30) REVERT: b 77 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8370 (m-30) REVERT: b 100 ASP cc_start: 0.8147 (t70) cc_final: 0.7941 (t70) REVERT: b 106 MET cc_start: 0.8863 (mtt) cc_final: 0.8345 (mtt) REVERT: b 151 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8185 (mm-30) REVERT: b 179 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8593 (mpt180) outliers start: 252 outliers final: 134 residues processed: 1146 average time/residue: 1.4205 time to fit residues: 2005.1938 Evaluate side-chains 1137 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 946 time to evaluate : 4.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 402 LYS Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain J residue 12 MET Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 201 LYS Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 186 ARG Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 260 LEU Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 6 PHE Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 97 ASP Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 20 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 220 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 172 GLN Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 237 LYS Chi-restraints excluded: chain Q residue 268 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 365 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 182 SER Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 188 GLU Chi-restraints excluded: chain U residue 227 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 241 GLN Chi-restraints excluded: chain V residue 252 MET Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain X residue 201 LYS Chi-restraints excluded: chain Y residue 11 LYS Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 129 MET Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain Z residue 249 GLU Chi-restraints excluded: chain Z residue 287 SER Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 198 LYS Chi-restraints excluded: chain a residue 253 VAL Chi-restraints excluded: chain b residue 68 GLU Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 179 ARG Chi-restraints excluded: chain b residue 192 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 574 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 339 optimal weight: 2.9990 chunk 435 optimal weight: 0.6980 chunk 337 optimal weight: 3.9990 chunk 501 optimal weight: 0.7980 chunk 332 optimal weight: 5.9990 chunk 593 optimal weight: 4.9990 chunk 371 optimal weight: 0.9990 chunk 361 optimal weight: 4.9990 chunk 274 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 228 ASN B 205 ASN D 18 GLN D 187 HIS F 206 ASN F 305 GLN F 371 ASN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 222 GLN ** L 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN O 228 ASN O 236 ASN P 205 ASN T 305 GLN U 64 ASN W 229 GLN Y 22 ASN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN a 130 GLN b 62 GLN b 94 GLN b 105 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 50122 Z= 0.227 Angle : 0.523 8.631 67810 Z= 0.279 Chirality : 0.042 0.189 7544 Planarity : 0.004 0.049 8790 Dihedral : 7.248 88.734 7135 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.88 % Favored : 98.04 % Rotamer: Outliers : 4.60 % Allowed : 21.61 % Favored : 73.79 % 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: 1.07 (0.10), residues: 6290 helix: 2.16 (0.10), residues: 2354 sheet: -0.07 (0.12), residues: 1564 loop : -0.13 (0.12), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 165 HIS 0.007 0.001 HIS D 187 PHE 0.016 0.001 PHE K 8 TYR 0.019 0.001 TYR J 96 ARG 0.008 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 965 time to evaluate : 4.228 Fit side-chains REVERT: A 125 GLN cc_start: 0.8015 (mt0) cc_final: 0.7616 (mm-40) REVERT: A 161 TRP cc_start: 0.8706 (t60) cc_final: 0.8251 (t-100) REVERT: A 184 ARG cc_start: 0.7966 (tpp80) cc_final: 0.7430 (mmm160) REVERT: A 215 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8126 (mmmt) REVERT: A 217 LYS cc_start: 0.8651 (tttt) cc_final: 0.8061 (pttt) REVERT: B 3 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6780 (tt0) REVERT: B 118 GLU cc_start: 0.8452 (tt0) cc_final: 0.8116 (tt0) REVERT: C 40 LYS cc_start: 0.8524 (mmtp) cc_final: 0.7927 (pttt) REVERT: C 237 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8253 (tppt) REVERT: C 263 GLN cc_start: 0.7312 (mt0) cc_final: 0.6895 (mt0) REVERT: C 265 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7477 (tpt-90) REVERT: C 266 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6946 (pt0) REVERT: D 4 ASP cc_start: 0.8208 (p0) cc_final: 0.7983 (p0) REVERT: D 18 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.7477 (mp-120) REVERT: D 52 LYS cc_start: 0.7992 (mttp) cc_final: 0.7580 (mppt) REVERT: D 57 ARG cc_start: 0.7652 (tmm160) cc_final: 0.7100 (ptt90) REVERT: D 166 GLN cc_start: 0.7894 (tp40) cc_final: 0.7665 (tp40) REVERT: D 174 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8262 (mtmm) REVERT: D 177 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7923 (mmtp) REVERT: D 180 MET cc_start: 0.8265 (mtt) cc_final: 0.7888 (mtm) REVERT: D 215 ARG cc_start: 0.8456 (ttp-170) cc_final: 0.7991 (mtp-110) REVERT: D 221 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7123 (tp30) REVERT: D 232 GLU cc_start: 0.7287 (tt0) cc_final: 0.6883 (mt-10) REVERT: E 107 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.5938 (mp0) REVERT: E 140 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8581 (mm) REVERT: E 190 GLU cc_start: 0.8443 (tp30) cc_final: 0.8152 (tp30) REVERT: E 278 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7417 (mt0) REVERT: E 300 ASP cc_start: 0.7987 (m-30) cc_final: 0.7387 (m-30) REVERT: E 342 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.5915 (ttm) REVERT: F 237 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8227 (ttm) REVERT: F 270 MET cc_start: 0.8931 (mmm) cc_final: 0.8579 (mmm) REVERT: F 402 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6890 (tptp) REVERT: G 13 ASP cc_start: 0.8845 (p0) cc_final: 0.8638 (p0) REVERT: G 43 LYS cc_start: 0.8679 (mmtp) cc_final: 0.8406 (mmmt) REVERT: G 51 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: G 115 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8131 (mpt-90) REVERT: G 184 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7594 (pt) REVERT: H 123 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8553 (p0) REVERT: H 139 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8210 (ttpp) REVERT: H 140 MET cc_start: 0.8936 (mmm) cc_final: 0.8518 (mpt) REVERT: H 143 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8068 (mpm) REVERT: H 201 MET cc_start: 0.8866 (mtt) cc_final: 0.8495 (mtp) REVERT: H 279 MET cc_start: 0.8903 (mtm) cc_final: 0.8486 (mtp) REVERT: I 59 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.7984 (mtm-85) REVERT: I 120 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8327 (mt0) REVERT: I 225 MET cc_start: 0.7177 (mtp) cc_final: 0.6779 (mtt) REVERT: I 226 TYR cc_start: 0.7188 (t80) cc_final: 0.6582 (t80) REVERT: I 230 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7814 (mm-30) REVERT: J 4 MET cc_start: 0.9115 (mmm) cc_final: 0.8841 (mmt) REVERT: J 38 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8543 (mm-30) REVERT: J 75 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8646 (mmtt) REVERT: J 97 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8164 (mt-10) REVERT: J 114 LYS cc_start: 0.8087 (tttt) cc_final: 0.7681 (mmtm) REVERT: K 1 MET cc_start: 0.7540 (mmm) cc_final: 0.7109 (mmm) REVERT: K 77 SER cc_start: 0.8837 (p) cc_final: 0.8627 (p) REVERT: K 129 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8328 (mtp) REVERT: K 181 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8678 (mpt180) REVERT: K 196 LYS cc_start: 0.8719 (ptmm) cc_final: 0.8478 (ptmt) REVERT: K 200 GLU cc_start: 0.8894 (pt0) cc_final: 0.8517 (pt0) REVERT: K 206 HIS cc_start: 0.8278 (p90) cc_final: 0.8006 (p-80) REVERT: L 134 LEU cc_start: 0.9076 (tt) cc_final: 0.8457 (mp) REVERT: L 155 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: L 191 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.7918 (m110) REVERT: M 174 TYR cc_start: 0.8835 (m-10) cc_final: 0.8140 (m-10) REVERT: M 186 ARG cc_start: 0.9320 (OUTLIER) cc_final: 0.8084 (ttm110) REVERT: M 226 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7264 (ptp-170) REVERT: M 240 ASP cc_start: 0.8645 (p0) cc_final: 0.8390 (p0) REVERT: M 296 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8675 (mt-10) REVERT: M 332 GLU cc_start: 0.8277 (pt0) cc_final: 0.8034 (pt0) REVERT: N 69 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8181 (mtt90) REVERT: N 106 MET cc_start: 0.8800 (mpt) cc_final: 0.8058 (mpt) REVERT: N 148 GLN cc_start: 0.8883 (tt0) cc_final: 0.8622 (tt0) REVERT: N 183 LYS cc_start: 0.8913 (ttpt) cc_final: 0.8698 (tppp) REVERT: N 195 ARG cc_start: 0.8672 (mtp-110) cc_final: 0.8282 (mtp85) REVERT: N 203 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7923 (mt-10) REVERT: O 7 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7279 (p0) REVERT: O 93 GLU cc_start: 0.8165 (tt0) cc_final: 0.7636 (tm-30) REVERT: O 97 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: O 115 MET cc_start: 0.9231 (mmm) cc_final: 0.8967 (mmp) REVERT: O 125 GLN cc_start: 0.8275 (mt0) cc_final: 0.8070 (tt0) REVERT: O 178 MET cc_start: 0.9151 (mmp) cc_final: 0.8946 (tpt) REVERT: O 190 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8356 (mp) REVERT: O 240 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7986 (mm-30) REVERT: P 16 LYS cc_start: 0.8825 (ptmt) cc_final: 0.8081 (mmtm) REVERT: P 98 MET cc_start: 0.8846 (tpp) cc_final: 0.8526 (ttp) REVERT: P 202 THR cc_start: 0.9014 (p) cc_final: 0.8597 (t) REVERT: P 226 ASP cc_start: 0.7915 (m-30) cc_final: 0.7703 (t70) REVERT: Q 15 GLU cc_start: 0.8285 (tt0) cc_final: 0.8031 (tp30) REVERT: Q 53 HIS cc_start: 0.8749 (t-90) cc_final: 0.8348 (t-90) REVERT: Q 59 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8346 (pt0) REVERT: Q 193 ASP cc_start: 0.8435 (t0) cc_final: 0.8184 (m-30) REVERT: Q 200 ARG cc_start: 0.8682 (mtm110) cc_final: 0.8361 (mtm-85) REVERT: Q 204 LYS cc_start: 0.8642 (tttt) cc_final: 0.8285 (tptp) REVERT: Q 266 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6708 (tm-30) REVERT: R 23 GLN cc_start: 0.8176 (mt0) cc_final: 0.7860 (mm-40) REVERT: R 54 GLN cc_start: 0.8077 (pt0) cc_final: 0.7499 (mm110) REVERT: R 59 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7625 (mp) REVERT: R 174 LYS cc_start: 0.7893 (mmtp) cc_final: 0.7518 (mtmm) REVERT: R 213 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7770 (mp0) REVERT: R 219 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: S 137 SER cc_start: 0.8731 (m) cc_final: 0.8527 (p) REVERT: S 249 LYS cc_start: 0.8701 (mmtm) cc_final: 0.8339 (mmmt) REVERT: S 336 LYS cc_start: 0.7987 (tttt) cc_final: 0.7527 (tppp) REVERT: T 343 HIS cc_start: 0.7244 (m90) cc_final: 0.6864 (m-70) REVERT: T 347 CYS cc_start: 0.8694 (m) cc_final: 0.8322 (m) REVERT: T 404 ARG cc_start: 0.5786 (OUTLIER) cc_final: 0.5304 (ppt170) REVERT: U 29 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8210 (mtmt) REVERT: U 94 GLN cc_start: 0.8570 (tt0) cc_final: 0.8355 (tm-30) REVERT: U 115 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8458 (mmt90) REVERT: U 185 THR cc_start: 0.8934 (p) cc_final: 0.8646 (p) REVERT: U 188 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8319 (pt0) REVERT: V 143 MET cc_start: 0.8494 (ttp) cc_final: 0.8153 (mmp) REVERT: V 201 MET cc_start: 0.8754 (mtt) cc_final: 0.8477 (mtm) REVERT: V 273 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8098 (tppt) REVERT: W 61 ARG cc_start: 0.7737 (mtp85) cc_final: 0.7396 (mmt90) REVERT: W 82 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: W 87 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8338 (ptm) REVERT: W 118 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8412 (ttm110) REVERT: W 119 TYR cc_start: 0.8908 (m-80) cc_final: 0.8617 (m-80) REVERT: W 149 ASP cc_start: 0.8145 (m-30) cc_final: 0.7842 (m-30) REVERT: X 6 TYR cc_start: 0.9031 (t80) cc_final: 0.8755 (t80) REVERT: X 14 MET cc_start: 0.8760 (mtt) cc_final: 0.8524 (mtt) REVERT: X 38 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8712 (mm-30) REVERT: X 78 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: X 134 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8153 (pm20) REVERT: X 191 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8363 (p) REVERT: Y 145 TYR cc_start: 0.8892 (m-10) cc_final: 0.8605 (m-80) REVERT: Y 200 GLU cc_start: 0.8845 (pt0) cc_final: 0.8415 (pt0) REVERT: Z 131 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8106 (mmt) REVERT: Z 191 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7729 (m110) REVERT: Z 196 MET cc_start: 0.8970 (ptp) cc_final: 0.8600 (ptm) REVERT: Z 244 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8343 (mmtt) REVERT: Z 249 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8387 (mm-30) REVERT: Z 280 GLU cc_start: 0.8248 (pt0) cc_final: 0.7820 (mp0) REVERT: Z 281 LYS cc_start: 0.8724 (mttm) cc_final: 0.8390 (mtmt) REVERT: a 198 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8482 (mttt) REVERT: a 242 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8167 (mm-30) REVERT: a 295 GLU cc_start: 0.8384 (mp0) cc_final: 0.8013 (mp0) REVERT: b 68 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8403 (tp30) REVERT: b 77 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8365 (m-30) REVERT: b 106 MET cc_start: 0.8889 (mtt) cc_final: 0.8384 (mtt) REVERT: b 151 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: b 179 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8551 (mpt180) outliers start: 241 outliers final: 133 residues processed: 1111 average time/residue: 1.4260 time to fit residues: 1946.9980 Evaluate side-chains 1129 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 945 time to evaluate : 4.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 402 LYS Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain J residue 12 MET Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 201 LYS Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 186 ARG Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 260 LEU Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 97 ASP Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 220 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 172 GLN Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 268 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 365 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 51 GLU Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 182 SER Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 188 GLU Chi-restraints excluded: chain U residue 227 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 252 MET Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain X residue 201 LYS Chi-restraints excluded: chain Y residue 11 LYS Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 45 VAL Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 152 GLN Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain Z residue 249 GLU Chi-restraints excluded: chain Z residue 291 GLN Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 198 LYS Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain a residue 253 VAL Chi-restraints excluded: chain a residue 327 ASP Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 68 GLU Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 179 ARG Chi-restraints excluded: chain b residue 192 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 367 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 354 optimal weight: 9.9990 chunk 178 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 377 optimal weight: 1.9990 chunk 404 optimal weight: 0.9990 chunk 293 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 466 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 228 ASN B 205 ASN D 18 GLN D 54 GLN D 187 HIS F 206 ASN F 305 GLN G 147 GLN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 222 GLN L 291 GLN O 228 ASN O 236 ASN P 200 GLN P 205 ASN R 223 GLN T 305 GLN V 241 GLN W 229 GLN Y 72 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 130 GLN b 62 GLN b 75 ASN b 94 GLN b 105 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 50122 Z= 0.235 Angle : 0.530 8.600 67810 Z= 0.281 Chirality : 0.042 0.193 7544 Planarity : 0.004 0.050 8790 Dihedral : 7.118 88.895 7123 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.91 % Favored : 98.03 % Rotamer: Outliers : 4.64 % Allowed : 21.95 % Favored : 73.41 % 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: 1.07 (0.10), residues: 6290 helix: 2.15 (0.10), residues: 2356 sheet: -0.06 (0.12), residues: 1566 loop : -0.12 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 165 HIS 0.007 0.001 HIS D 187 PHE 0.019 0.001 PHE K 8 TYR 0.020 0.001 TYR J 96 ARG 0.007 0.000 ARG N 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 969 time to evaluate : 4.303 Fit side-chains REVERT: A 42 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7807 (ptpt) REVERT: A 61 ASP cc_start: 0.8256 (t0) cc_final: 0.7991 (p0) REVERT: A 125 GLN cc_start: 0.7993 (mt0) cc_final: 0.7609 (mm-40) REVERT: A 161 TRP cc_start: 0.8735 (t60) cc_final: 0.8237 (t-100) REVERT: A 184 ARG cc_start: 0.7984 (tpp80) cc_final: 0.7412 (mmm160) REVERT: A 215 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8084 (mmmt) REVERT: A 217 LYS cc_start: 0.8638 (tttt) cc_final: 0.8052 (pttp) REVERT: B 118 GLU cc_start: 0.8459 (tt0) cc_final: 0.8110 (tt0) REVERT: C 40 LYS cc_start: 0.8545 (mmtp) cc_final: 0.7962 (pttt) REVERT: C 187 GLU cc_start: 0.7687 (pm20) cc_final: 0.7472 (pm20) REVERT: C 237 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8321 (tppt) REVERT: C 263 GLN cc_start: 0.7310 (mt0) cc_final: 0.6893 (mt0) REVERT: C 265 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7443 (tpt-90) REVERT: C 266 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6947 (pt0) REVERT: D 4 ASP cc_start: 0.8209 (p0) cc_final: 0.7973 (p0) REVERT: D 52 LYS cc_start: 0.7934 (mttp) cc_final: 0.7534 (mppt) REVERT: D 57 ARG cc_start: 0.7653 (tmm160) cc_final: 0.7090 (ptt90) REVERT: D 138 GLU cc_start: 0.8620 (tp30) cc_final: 0.8389 (mm-30) REVERT: D 166 GLN cc_start: 0.7917 (tp40) cc_final: 0.7662 (tp40) REVERT: D 174 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8313 (mtmm) REVERT: D 177 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7923 (mmtp) REVERT: D 180 MET cc_start: 0.8267 (mtt) cc_final: 0.7896 (mtm) REVERT: D 215 ARG cc_start: 0.8457 (ttp-170) cc_final: 0.8000 (mtp-110) REVERT: D 221 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7105 (tp30) REVERT: D 232 GLU cc_start: 0.7281 (tt0) cc_final: 0.6886 (mt-10) REVERT: E 107 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.5970 (mp0) REVERT: E 140 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8568 (mm) REVERT: E 190 GLU cc_start: 0.8447 (tp30) cc_final: 0.8172 (tp30) REVERT: E 278 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7414 (mt0) REVERT: E 300 ASP cc_start: 0.7992 (m-30) cc_final: 0.7407 (m-30) REVERT: E 342 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.5903 (ttm) REVERT: F 237 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8205 (ttm) REVERT: F 270 MET cc_start: 0.8937 (mmm) cc_final: 0.8548 (mmm) REVERT: F 402 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6791 (tptp) REVERT: G 13 ASP cc_start: 0.8874 (p0) cc_final: 0.8658 (p0) REVERT: G 43 LYS cc_start: 0.8683 (mmtp) cc_final: 0.8121 (mtmp) REVERT: G 51 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: G 115 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8161 (mpt-90) REVERT: G 184 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7587 (pt) REVERT: H 123 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8573 (p0) REVERT: H 139 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8202 (ttpp) REVERT: H 140 MET cc_start: 0.8875 (mmm) cc_final: 0.8470 (mpt) REVERT: H 143 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8063 (mpm) REVERT: H 201 MET cc_start: 0.8875 (mtt) cc_final: 0.8506 (mtp) REVERT: H 279 MET cc_start: 0.8903 (mtm) cc_final: 0.8496 (mtp) REVERT: I 120 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8266 (mt0) REVERT: I 225 MET cc_start: 0.7054 (mtp) cc_final: 0.6695 (mtt) REVERT: I 226 TYR cc_start: 0.7181 (t80) cc_final: 0.6582 (t80) REVERT: I 230 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7828 (mm-30) REVERT: J 4 MET cc_start: 0.9111 (mmm) cc_final: 0.8836 (mmt) REVERT: J 38 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8541 (mm-30) REVERT: J 75 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8624 (mmtt) REVERT: J 97 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8114 (mt-10) REVERT: J 114 LYS cc_start: 0.8087 (tttt) cc_final: 0.7682 (mmtm) REVERT: K 1 MET cc_start: 0.7538 (mmm) cc_final: 0.7111 (mmm) REVERT: K 50 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: K 77 SER cc_start: 0.8840 (p) cc_final: 0.8630 (p) REVERT: K 129 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8325 (mtp) REVERT: K 196 LYS cc_start: 0.8711 (ptmm) cc_final: 0.8508 (ptmt) REVERT: K 200 GLU cc_start: 0.8877 (pt0) cc_final: 0.8547 (pt0) REVERT: K 206 HIS cc_start: 0.8284 (p90) cc_final: 0.8029 (p-80) REVERT: L 134 LEU cc_start: 0.9078 (tt) cc_final: 0.8471 (mp) REVERT: L 155 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: L 191 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7928 (m110) REVERT: M 174 TYR cc_start: 0.8840 (m-10) cc_final: 0.8131 (m-10) REVERT: M 186 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.8090 (ttm110) REVERT: M 226 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7297 (ptp-170) REVERT: M 240 ASP cc_start: 0.8619 (p0) cc_final: 0.8341 (p0) REVERT: M 257 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8757 (pt0) REVERT: M 292 MET cc_start: 0.8335 (tpp) cc_final: 0.8057 (tpp) REVERT: M 296 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8608 (mt-10) REVERT: M 332 GLU cc_start: 0.8258 (pt0) cc_final: 0.8012 (pt0) REVERT: N 69 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8084 (mtt90) REVERT: N 106 MET cc_start: 0.8788 (mpt) cc_final: 0.8127 (mpt) REVERT: N 148 GLN cc_start: 0.8883 (tt0) cc_final: 0.8620 (tt0) REVERT: N 183 LYS cc_start: 0.8905 (ttpt) cc_final: 0.8695 (tppp) REVERT: N 195 ARG cc_start: 0.8675 (mtp-110) cc_final: 0.8274 (mtp85) REVERT: N 203 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: O 7 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7252 (p0) REVERT: O 93 GLU cc_start: 0.8143 (tt0) cc_final: 0.7581 (mt-10) REVERT: O 97 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: O 115 MET cc_start: 0.9229 (mmm) cc_final: 0.8969 (mmp) REVERT: O 125 GLN cc_start: 0.8272 (mt0) cc_final: 0.8065 (tt0) REVERT: O 190 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8358 (mp) REVERT: O 240 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8036 (mm-30) REVERT: P 16 LYS cc_start: 0.8833 (ptmt) cc_final: 0.8077 (mmtm) REVERT: P 202 THR cc_start: 0.8976 (p) cc_final: 0.8560 (t) REVERT: Q 15 GLU cc_start: 0.8241 (tt0) cc_final: 0.8023 (tp30) REVERT: Q 53 HIS cc_start: 0.8766 (t-90) cc_final: 0.8343 (t-90) REVERT: Q 59 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8327 (pt0) REVERT: Q 193 ASP cc_start: 0.8434 (t0) cc_final: 0.8182 (m-30) REVERT: Q 200 ARG cc_start: 0.8689 (mtm110) cc_final: 0.8343 (mtm-85) REVERT: Q 204 LYS cc_start: 0.8643 (tttt) cc_final: 0.8288 (tptp) REVERT: Q 266 GLU cc_start: 0.6881 (tm-30) cc_final: 0.6665 (tm-30) REVERT: R 23 GLN cc_start: 0.8181 (mt0) cc_final: 0.7862 (mm-40) REVERT: R 49 SER cc_start: 0.6373 (t) cc_final: 0.5923 (p) REVERT: R 54 GLN cc_start: 0.8040 (pt0) cc_final: 0.7500 (mm110) REVERT: R 59 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7630 (mp) REVERT: R 174 LYS cc_start: 0.7907 (mmtp) cc_final: 0.7528 (mtmm) REVERT: R 213 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7840 (mp0) REVERT: R 219 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: R 223 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6919 (mm110) REVERT: S 249 LYS cc_start: 0.8703 (mmtm) cc_final: 0.8330 (mmmt) REVERT: S 336 LYS cc_start: 0.7991 (tttt) cc_final: 0.7554 (tppp) REVERT: T 190 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7718 (m-40) REVERT: T 343 HIS cc_start: 0.7237 (m90) cc_final: 0.6878 (m-70) REVERT: T 347 CYS cc_start: 0.8694 (m) cc_final: 0.8323 (m) REVERT: T 404 ARG cc_start: 0.5824 (OUTLIER) cc_final: 0.5337 (ppt170) REVERT: U 94 GLN cc_start: 0.8502 (tt0) cc_final: 0.8281 (tm-30) REVERT: U 115 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8475 (mmt90) REVERT: U 185 THR cc_start: 0.8941 (p) cc_final: 0.8652 (p) REVERT: U 188 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: V 143 MET cc_start: 0.8491 (ttp) cc_final: 0.8150 (mmp) REVERT: V 201 MET cc_start: 0.8751 (mtt) cc_final: 0.8476 (mtm) REVERT: V 273 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8096 (tppt) REVERT: W 51 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: W 61 ARG cc_start: 0.7748 (mtp85) cc_final: 0.7432 (mmt180) REVERT: W 82 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8462 (tt0) REVERT: W 87 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8345 (ptm) REVERT: W 118 ARG cc_start: 0.8812 (ttp80) cc_final: 0.8420 (ttm110) REVERT: W 119 TYR cc_start: 0.8904 (m-80) cc_final: 0.8689 (m-80) REVERT: W 149 ASP cc_start: 0.8156 (m-30) cc_final: 0.7852 (m-30) REVERT: W 230 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6902 (mm-30) REVERT: X 6 TYR cc_start: 0.9027 (t80) cc_final: 0.8747 (t80) REVERT: X 14 MET cc_start: 0.8759 (mtt) cc_final: 0.8506 (mtt) REVERT: X 17 LYS cc_start: 0.8887 (tttt) cc_final: 0.8586 (ttmm) REVERT: X 38 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8708 (mm-30) REVERT: X 78 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: X 134 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: X 191 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8373 (p) REVERT: Y 145 TYR cc_start: 0.8887 (m-10) cc_final: 0.8601 (m-80) REVERT: Y 200 GLU cc_start: 0.8825 (pt0) cc_final: 0.8409 (pt0) REVERT: Z 131 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8089 (mmt) REVERT: Z 191 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7736 (m110) REVERT: Z 196 MET cc_start: 0.8916 (ptp) cc_final: 0.8655 (ptm) REVERT: Z 244 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8339 (mmtt) REVERT: Z 249 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8375 (mm-30) REVERT: Z 280 GLU cc_start: 0.8249 (pt0) cc_final: 0.7825 (mp0) REVERT: Z 281 LYS cc_start: 0.8677 (mttm) cc_final: 0.8333 (mtmt) REVERT: Z 287 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8507 (p) REVERT: a 198 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8484 (mttt) REVERT: a 242 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8161 (mm-30) REVERT: a 295 GLU cc_start: 0.8436 (mp0) cc_final: 0.8057 (mp0) REVERT: b 13 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8342 (mtpt) REVERT: b 68 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8385 (tp30) REVERT: b 77 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8360 (m-30) REVERT: b 106 MET cc_start: 0.8912 (mtt) cc_final: 0.8429 (mtt) REVERT: b 115 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7260 (tm-30) REVERT: b 151 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8096 (mm-30) outliers start: 243 outliers final: 131 residues processed: 1116 average time/residue: 1.4520 time to fit residues: 1991.0654 Evaluate side-chains 1126 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 940 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 402 LYS Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain J residue 12 MET Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 201 LYS Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 186 ARG Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 260 LEU Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain M residue 338 LYS Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 152 LYS Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 97 ASP Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 220 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 172 GLN Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 237 LYS Chi-restraints excluded: chain Q residue 268 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 98 TYR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 223 GLN Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 365 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 51 GLU Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 182 SER Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 188 GLU Chi-restraints excluded: chain U residue 227 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 252 MET Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 51 GLU Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 230 GLU Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain X residue 201 LYS Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 152 GLN Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain Z residue 249 GLU Chi-restraints excluded: chain Z residue 287 SER Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 198 LYS Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain a residue 253 VAL Chi-restraints excluded: chain a residue 327 ASP Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 13 LYS Chi-restraints excluded: chain b residue 68 GLU Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 192 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 540 optimal weight: 3.9990 chunk 568 optimal weight: 1.9990 chunk 518 optimal weight: 0.8980 chunk 553 optimal weight: 1.9990 chunk 333 optimal weight: 0.0060 chunk 241 optimal weight: 0.9980 chunk 434 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 499 optimal weight: 1.9990 chunk 523 optimal weight: 0.9990 chunk 551 optimal weight: 2.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 228 ASN B 19 GLN B 205 ASN C 62 GLN D 18 GLN D 54 GLN D 187 HIS F 206 ASN F 305 GLN F 371 ASN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN L 222 GLN L 291 GLN O 228 ASN O 236 ASN P 205 ASN R 223 GLN S 191 HIS T 305 GLN U 64 ASN V 241 GLN W 229 GLN X 169 GLN Y 22 ASN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 130 GLN b 62 GLN b 94 GLN b 105 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 50122 Z= 0.182 Angle : 0.512 9.457 67810 Z= 0.272 Chirality : 0.042 0.180 7544 Planarity : 0.004 0.049 8790 Dihedral : 6.842 89.004 7112 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.73 % Favored : 98.20 % Rotamer: Outliers : 3.61 % Allowed : 23.14 % Favored : 73.25 % 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: 1.14 (0.10), residues: 6290 helix: 2.22 (0.10), residues: 2356 sheet: -0.00 (0.12), residues: 1548 loop : -0.12 (0.12), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 154 HIS 0.007 0.001 HIS D 187 PHE 0.016 0.001 PHE K 8 TYR 0.021 0.001 TYR J 96 ARG 0.008 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1001 time to evaluate : 4.334 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8253 (t0) cc_final: 0.7996 (p0) REVERT: A 125 GLN cc_start: 0.7974 (mt0) cc_final: 0.7578 (mm-40) REVERT: A 161 TRP cc_start: 0.8718 (t60) cc_final: 0.8246 (t-100) REVERT: A 184 ARG cc_start: 0.7900 (tpp80) cc_final: 0.7390 (mmm160) REVERT: A 217 LYS cc_start: 0.8470 (tttt) cc_final: 0.7986 (pptt) REVERT: B 3 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7008 (tt0) REVERT: B 118 GLU cc_start: 0.8385 (tt0) cc_final: 0.8073 (tt0) REVERT: C 40 LYS cc_start: 0.8584 (mmtp) cc_final: 0.8048 (pttt) REVERT: C 187 GLU cc_start: 0.7618 (pm20) cc_final: 0.7401 (pm20) REVERT: C 196 LEU cc_start: 0.9057 (tp) cc_final: 0.8817 (tt) REVERT: C 237 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8304 (tppt) REVERT: C 263 GLN cc_start: 0.7299 (mt0) cc_final: 0.6880 (mt0) REVERT: C 265 ARG cc_start: 0.7722 (tpp-160) cc_final: 0.7453 (tpt-90) REVERT: C 266 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6937 (pt0) REVERT: D 52 LYS cc_start: 0.7901 (mttp) cc_final: 0.7468 (mppt) REVERT: D 57 ARG cc_start: 0.7628 (tmm160) cc_final: 0.7035 (ptt90) REVERT: D 138 GLU cc_start: 0.8577 (tp30) cc_final: 0.8331 (mm-30) REVERT: D 166 GLN cc_start: 0.7872 (tp40) cc_final: 0.7646 (tp40) REVERT: D 174 LYS cc_start: 0.8696 (mtmt) cc_final: 0.8326 (mtmm) REVERT: D 177 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7951 (mmtp) REVERT: D 180 MET cc_start: 0.8256 (mtt) cc_final: 0.7898 (mtm) REVERT: D 203 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7533 (p0) REVERT: D 215 ARG cc_start: 0.8434 (ttp-170) cc_final: 0.7957 (mtp-110) REVERT: D 221 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7022 (tp30) REVERT: D 232 GLU cc_start: 0.7224 (tt0) cc_final: 0.6836 (mt-10) REVERT: E 107 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.5974 (mp0) REVERT: E 140 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8556 (mm) REVERT: E 190 GLU cc_start: 0.8442 (tp30) cc_final: 0.8164 (tp30) REVERT: E 300 ASP cc_start: 0.7983 (m-30) cc_final: 0.7401 (m-30) REVERT: E 342 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.6062 (ttm) REVERT: F 270 MET cc_start: 0.8854 (mmm) cc_final: 0.8473 (mmm) REVERT: F 339 ARG cc_start: 0.8383 (mtm-85) cc_final: 0.8179 (mtm-85) REVERT: F 369 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7331 (mm-30) REVERT: F 402 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6907 (tptp) REVERT: G 13 ASP cc_start: 0.8860 (p0) cc_final: 0.8646 (p0) REVERT: G 43 LYS cc_start: 0.8667 (mmtp) cc_final: 0.8127 (mtmp) REVERT: G 51 GLU cc_start: 0.8210 (tt0) cc_final: 0.7816 (tm-30) REVERT: G 115 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8229 (mpt-90) REVERT: H 123 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8569 (p0) REVERT: H 139 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8310 (ttpp) REVERT: H 140 MET cc_start: 0.8851 (mmm) cc_final: 0.8474 (mpt) REVERT: H 201 MET cc_start: 0.8824 (mtt) cc_final: 0.8488 (mtt) REVERT: H 279 MET cc_start: 0.8901 (mtm) cc_final: 0.8508 (mtp) REVERT: I 120 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8385 (mt0) REVERT: I 225 MET cc_start: 0.7107 (mtp) cc_final: 0.6769 (mtm) REVERT: I 226 TYR cc_start: 0.7205 (t80) cc_final: 0.6571 (t80) REVERT: I 230 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7736 (mp0) REVERT: J 4 MET cc_start: 0.9071 (mmm) cc_final: 0.8772 (mmt) REVERT: J 38 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8539 (mm-30) REVERT: J 75 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8667 (mmtt) REVERT: J 97 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8120 (mt-10) REVERT: J 114 LYS cc_start: 0.8032 (tttt) cc_final: 0.7669 (mmtm) REVERT: J 201 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8552 (ttpt) REVERT: K 1 MET cc_start: 0.7517 (mmm) cc_final: 0.7100 (mmm) REVERT: K 50 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: K 196 LYS cc_start: 0.8684 (ptmm) cc_final: 0.8443 (ptmt) REVERT: K 200 GLU cc_start: 0.8847 (pt0) cc_final: 0.8486 (pt0) REVERT: K 206 HIS cc_start: 0.8240 (p90) cc_final: 0.7993 (p-80) REVERT: L 134 LEU cc_start: 0.9036 (tt) cc_final: 0.8448 (mp) REVERT: L 155 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: L 249 GLU cc_start: 0.8694 (tp30) cc_final: 0.8027 (mp0) REVERT: M 174 TYR cc_start: 0.8840 (m-10) cc_final: 0.8090 (m-10) REVERT: M 186 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.7990 (ttm110) REVERT: M 240 ASP cc_start: 0.8515 (p0) cc_final: 0.8273 (p0) REVERT: M 257 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8730 (pt0) REVERT: M 263 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.9126 (t) REVERT: M 332 GLU cc_start: 0.8301 (pt0) cc_final: 0.8021 (pt0) REVERT: N 34 ASN cc_start: 0.9358 (p0) cc_final: 0.9076 (p0) REVERT: N 69 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8041 (mtt90) REVERT: N 106 MET cc_start: 0.8750 (mpt) cc_final: 0.8019 (mpt) REVERT: N 148 GLN cc_start: 0.8834 (tt0) cc_final: 0.8578 (tt0) REVERT: N 183 LYS cc_start: 0.8880 (ttpt) cc_final: 0.8679 (tppp) REVERT: N 195 ARG cc_start: 0.8667 (mtp-110) cc_final: 0.8320 (mtp85) REVERT: N 203 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7918 (mt-10) REVERT: O 7 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7258 (p0) REVERT: O 36 THR cc_start: 0.8964 (p) cc_final: 0.8720 (t) REVERT: O 93 GLU cc_start: 0.8176 (tt0) cc_final: 0.7627 (mt-10) REVERT: O 97 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: O 115 MET cc_start: 0.9205 (mmm) cc_final: 0.8932 (mmp) REVERT: O 125 GLN cc_start: 0.8245 (mt0) cc_final: 0.8041 (tt0) REVERT: O 190 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8286 (mp) REVERT: O 240 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8042 (mm-30) REVERT: P 16 LYS cc_start: 0.8796 (ptmt) cc_final: 0.8053 (mmtm) REVERT: P 202 THR cc_start: 0.8984 (p) cc_final: 0.8585 (t) REVERT: Q 53 HIS cc_start: 0.8755 (t-90) cc_final: 0.8331 (t-90) REVERT: Q 193 ASP cc_start: 0.8423 (t0) cc_final: 0.8194 (m-30) REVERT: Q 200 ARG cc_start: 0.8696 (mtm110) cc_final: 0.8349 (mtm-85) REVERT: Q 204 LYS cc_start: 0.8627 (tttt) cc_final: 0.8282 (tptp) REVERT: Q 266 GLU cc_start: 0.6899 (tm-30) cc_final: 0.6696 (tm-30) REVERT: R 23 GLN cc_start: 0.8169 (mt0) cc_final: 0.7840 (mm-40) REVERT: R 49 SER cc_start: 0.6264 (t) cc_final: 0.5843 (p) REVERT: R 54 GLN cc_start: 0.8039 (pt0) cc_final: 0.7511 (mm110) REVERT: R 59 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7430 (mp) REVERT: R 174 LYS cc_start: 0.7874 (mmtp) cc_final: 0.7538 (mtmm) REVERT: R 210 GLN cc_start: 0.9301 (mt0) cc_final: 0.9025 (mt0) REVERT: R 213 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7823 (mp0) REVERT: R 223 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6957 (mm110) REVERT: S 249 LYS cc_start: 0.8735 (mmtm) cc_final: 0.8386 (mmmt) REVERT: S 336 LYS cc_start: 0.7932 (tttt) cc_final: 0.7497 (tppp) REVERT: T 343 HIS cc_start: 0.7170 (m90) cc_final: 0.6793 (m-70) REVERT: T 347 CYS cc_start: 0.8645 (m) cc_final: 0.8284 (m) REVERT: T 404 ARG cc_start: 0.5814 (OUTLIER) cc_final: 0.5400 (ppt170) REVERT: U 94 GLN cc_start: 0.8491 (tt0) cc_final: 0.8247 (tm-30) REVERT: U 185 THR cc_start: 0.8932 (p) cc_final: 0.8655 (p) REVERT: U 188 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8381 (pt0) REVERT: V 143 MET cc_start: 0.8451 (ttp) cc_final: 0.8120 (mmp) REVERT: V 201 MET cc_start: 0.8679 (mtt) cc_final: 0.8414 (mtm) REVERT: V 273 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8066 (tppt) REVERT: W 61 ARG cc_start: 0.7708 (mtp85) cc_final: 0.7469 (mmt180) REVERT: W 82 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: W 87 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8339 (ptm) REVERT: W 118 ARG cc_start: 0.8796 (ttp80) cc_final: 0.8411 (ttm110) REVERT: W 230 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6943 (mm-30) REVERT: X 6 TYR cc_start: 0.9005 (t80) cc_final: 0.8716 (t80) REVERT: X 17 LYS cc_start: 0.8813 (tttt) cc_final: 0.8531 (ttmm) REVERT: X 38 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8651 (mm-30) REVERT: X 78 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: X 191 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8406 (p) REVERT: Y 200 GLU cc_start: 0.8794 (pt0) cc_final: 0.8378 (pt0) REVERT: Z 131 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8428 (tpp) REVERT: Z 196 MET cc_start: 0.8737 (ptp) cc_final: 0.8528 (ptm) REVERT: Z 244 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8299 (mmtt) REVERT: Z 280 GLU cc_start: 0.8249 (pt0) cc_final: 0.7823 (mp0) REVERT: Z 281 LYS cc_start: 0.8664 (mttm) cc_final: 0.8320 (mtmt) REVERT: Z 287 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8496 (p) REVERT: a 130 GLN cc_start: 0.8633 (tt0) cc_final: 0.8408 (tt0) REVERT: a 182 MET cc_start: 0.8925 (ttt) cc_final: 0.8607 (ttm) REVERT: a 198 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8477 (mttt) REVERT: a 242 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8136 (mm-30) REVERT: a 292 MET cc_start: 0.8350 (tpp) cc_final: 0.8061 (tpt) REVERT: a 317 ASP cc_start: 0.7599 (m-30) cc_final: 0.7352 (m-30) REVERT: b 13 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8325 (mtpt) REVERT: b 68 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8393 (tp30) REVERT: b 106 MET cc_start: 0.8906 (mtt) cc_final: 0.8429 (mtt) REVERT: b 115 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7202 (tm-30) REVERT: b 151 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8092 (mm-30) outliers start: 189 outliers final: 108 residues processed: 1112 average time/residue: 1.5266 time to fit residues: 2101.6356 Evaluate side-chains 1102 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 954 time to evaluate : 4.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 402 LYS Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain J residue 12 MET Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 201 LYS Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain M residue 186 ARG Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 260 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 152 LYS Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 97 ASP Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 20 ILE Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 220 SER Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 237 LYS Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 98 TYR Chi-restraints excluded: chain R residue 172 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 223 GLN Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 365 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 51 GLU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 188 GLU Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 230 GLU Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain X residue 201 LYS Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 45 VAL Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 152 GLN Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain Z residue 287 SER Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 198 LYS Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain a residue 327 ASP Chi-restraints excluded: chain b residue 13 LYS Chi-restraints excluded: chain b residue 68 GLU Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 151 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 363 optimal weight: 0.8980 chunk 585 optimal weight: 0.8980 chunk 357 optimal weight: 4.9990 chunk 277 optimal weight: 1.9990 chunk 406 optimal weight: 4.9990 chunk 613 optimal weight: 0.6980 chunk 564 optimal weight: 6.9990 chunk 488 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 377 optimal weight: 0.0270 chunk 299 optimal weight: 3.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 228 ASN B 19 GLN B 205 ASN C 62 GLN D 18 GLN D 143 HIS D 187 HIS ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN F 305 GLN G 147 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 GLN L 222 GLN ** L 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 228 ASN P 187 HIS P 200 GLN P 205 ASN R 187 HIS R 223 GLN T 266 ASN U 64 ASN V 241 GLN W 86 ASN W 229 GLN Y 72 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 ASN b 105 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 50122 Z= 0.199 Angle : 0.523 9.589 67810 Z= 0.277 Chirality : 0.042 0.189 7544 Planarity : 0.004 0.048 8790 Dihedral : 6.657 89.035 7091 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.99 % Favored : 97.95 % Rotamer: Outliers : 3.28 % Allowed : 23.84 % Favored : 72.87 % 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: 1.16 (0.10), residues: 6290 helix: 2.23 (0.10), residues: 2356 sheet: 0.01 (0.12), residues: 1548 loop : -0.10 (0.12), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 165 HIS 0.007 0.001 HIS D 187 PHE 0.016 0.001 PHE a 270 TYR 0.023 0.001 TYR J 96 ARG 0.010 0.000 ARG U 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1124 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 952 time to evaluate : 4.197 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8224 (t0) cc_final: 0.8007 (p0) REVERT: A 125 GLN cc_start: 0.7994 (mt0) cc_final: 0.7712 (tp40) REVERT: A 161 TRP cc_start: 0.8739 (t60) cc_final: 0.8223 (t-100) REVERT: A 165 HIS cc_start: 0.9046 (m-70) cc_final: 0.8615 (m-70) REVERT: A 184 ARG cc_start: 0.7900 (tpp80) cc_final: 0.7389 (mmm160) REVERT: A 217 LYS cc_start: 0.8463 (tttt) cc_final: 0.7994 (pttt) REVERT: B 3 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7028 (tt0) REVERT: B 118 GLU cc_start: 0.8401 (tt0) cc_final: 0.8088 (tt0) REVERT: C 40 LYS cc_start: 0.8534 (mmtp) cc_final: 0.7949 (pttt) REVERT: C 196 LEU cc_start: 0.9055 (tp) cc_final: 0.8815 (tt) REVERT: C 237 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8298 (tppt) REVERT: C 263 GLN cc_start: 0.7300 (mt0) cc_final: 0.6882 (mt0) REVERT: C 265 ARG cc_start: 0.7723 (tpp-160) cc_final: 0.7453 (tpt-90) REVERT: C 266 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6940 (pt0) REVERT: D 52 LYS cc_start: 0.7899 (mttp) cc_final: 0.7464 (mppt) REVERT: D 57 ARG cc_start: 0.7615 (tmm160) cc_final: 0.7030 (ptt90) REVERT: D 138 GLU cc_start: 0.8575 (tp30) cc_final: 0.8326 (mm-30) REVERT: D 166 GLN cc_start: 0.7871 (tp40) cc_final: 0.7646 (tp40) REVERT: D 174 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8334 (mtmm) REVERT: D 177 LYS cc_start: 0.8322 (mtpm) cc_final: 0.7946 (mmtp) REVERT: D 180 MET cc_start: 0.8257 (mtt) cc_final: 0.7896 (mtm) REVERT: D 203 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7609 (p0) REVERT: D 215 ARG cc_start: 0.8422 (ttp-170) cc_final: 0.7971 (mtp-110) REVERT: D 221 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7047 (tp30) REVERT: D 232 GLU cc_start: 0.7189 (tt0) cc_final: 0.6869 (mt-10) REVERT: E 140 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8567 (mm) REVERT: E 190 GLU cc_start: 0.8445 (tp30) cc_final: 0.8168 (tp30) REVERT: E 300 ASP cc_start: 0.7953 (m-30) cc_final: 0.7342 (m-30) REVERT: E 342 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.6029 (ttm) REVERT: F 270 MET cc_start: 0.8878 (mmm) cc_final: 0.8501 (mmm) REVERT: F 369 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7321 (mm-30) REVERT: F 402 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6929 (tptt) REVERT: G 13 ASP cc_start: 0.8874 (p0) cc_final: 0.8654 (p0) REVERT: G 43 LYS cc_start: 0.8665 (mmtp) cc_final: 0.8133 (mtmp) REVERT: G 51 GLU cc_start: 0.8215 (tt0) cc_final: 0.7811 (tm-30) REVERT: G 115 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8300 (mpt-90) REVERT: H 123 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8589 (p0) REVERT: H 139 LYS cc_start: 0.8693 (ttmm) cc_final: 0.8320 (ttpp) REVERT: H 140 MET cc_start: 0.8852 (mmm) cc_final: 0.8469 (mpt) REVERT: H 201 MET cc_start: 0.8833 (mtt) cc_final: 0.8509 (mtt) REVERT: H 279 MET cc_start: 0.8894 (mtm) cc_final: 0.8510 (mtp) REVERT: I 225 MET cc_start: 0.7057 (mtp) cc_final: 0.6743 (mtm) REVERT: I 226 TYR cc_start: 0.7228 (t80) cc_final: 0.6604 (t80) REVERT: I 230 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7535 (mm-30) REVERT: J 4 MET cc_start: 0.9075 (mmm) cc_final: 0.8781 (mmt) REVERT: J 38 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8530 (mm-30) REVERT: J 75 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8667 (mmtt) REVERT: J 97 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8123 (mt-10) REVERT: J 114 LYS cc_start: 0.8037 (tttt) cc_final: 0.7688 (mmtm) REVERT: J 201 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8545 (ttpt) REVERT: K 1 MET cc_start: 0.7514 (mmm) cc_final: 0.7076 (mmm) REVERT: K 50 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: K 196 LYS cc_start: 0.8682 (ptmm) cc_final: 0.8440 (ptmt) REVERT: K 200 GLU cc_start: 0.8832 (pt0) cc_final: 0.8485 (pt0) REVERT: K 206 HIS cc_start: 0.8242 (p90) cc_final: 0.7990 (p-80) REVERT: L 134 LEU cc_start: 0.9034 (tt) cc_final: 0.8448 (mp) REVERT: L 155 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: L 249 GLU cc_start: 0.8688 (tp30) cc_final: 0.8031 (mp0) REVERT: M 174 TYR cc_start: 0.8825 (m-10) cc_final: 0.8104 (m-10) REVERT: M 186 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.8222 (ttm110) REVERT: M 240 ASP cc_start: 0.8491 (p0) cc_final: 0.8254 (p0) REVERT: M 257 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8749 (pt0) REVERT: M 332 GLU cc_start: 0.8320 (pt0) cc_final: 0.8028 (pt0) REVERT: N 69 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8027 (mtt90) REVERT: N 106 MET cc_start: 0.8750 (mpt) cc_final: 0.8087 (mpt) REVERT: N 148 GLN cc_start: 0.8852 (tt0) cc_final: 0.8606 (tt0) REVERT: N 183 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8682 (tppp) REVERT: N 195 ARG cc_start: 0.8667 (mtp-110) cc_final: 0.8311 (mtp85) REVERT: N 203 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: O 7 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7257 (p0) REVERT: O 36 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8733 (t) REVERT: O 93 GLU cc_start: 0.8157 (tt0) cc_final: 0.7528 (tm-30) REVERT: O 97 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: O 115 MET cc_start: 0.9215 (mmm) cc_final: 0.8947 (mmp) REVERT: O 125 GLN cc_start: 0.8249 (mt0) cc_final: 0.8020 (tt0) REVERT: O 178 MET cc_start: 0.8955 (mmm) cc_final: 0.8752 (tpt) REVERT: O 190 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8276 (mp) REVERT: O 240 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8074 (mm-30) REVERT: P 16 LYS cc_start: 0.8793 (ptmt) cc_final: 0.8055 (mmtm) REVERT: P 202 THR cc_start: 0.8941 (p) cc_final: 0.8552 (t) REVERT: Q 53 HIS cc_start: 0.8761 (t-90) cc_final: 0.8340 (t-90) REVERT: Q 193 ASP cc_start: 0.8423 (t0) cc_final: 0.8199 (m-30) REVERT: Q 200 ARG cc_start: 0.8695 (mtm110) cc_final: 0.8346 (mtm-85) REVERT: Q 204 LYS cc_start: 0.8562 (tttt) cc_final: 0.8256 (tptp) REVERT: Q 266 GLU cc_start: 0.6899 (tm-30) cc_final: 0.6689 (tm-30) REVERT: R 23 GLN cc_start: 0.8165 (mt0) cc_final: 0.7846 (mm-40) REVERT: R 49 SER cc_start: 0.6245 (t) cc_final: 0.5836 (p) REVERT: R 54 GLN cc_start: 0.8022 (pt0) cc_final: 0.7668 (tp-100) REVERT: R 174 LYS cc_start: 0.7839 (mmtp) cc_final: 0.7503 (mtmm) REVERT: R 213 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7787 (mp0) REVERT: R 223 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6831 (mm110) REVERT: S 249 LYS cc_start: 0.8740 (mmtm) cc_final: 0.8382 (mmmt) REVERT: S 313 GLU cc_start: 0.8777 (mp0) cc_final: 0.8576 (mp0) REVERT: S 336 LYS cc_start: 0.7967 (tttt) cc_final: 0.7534 (tppp) REVERT: T 343 HIS cc_start: 0.7176 (m90) cc_final: 0.6777 (m-70) REVERT: T 347 CYS cc_start: 0.8623 (m) cc_final: 0.8260 (m) REVERT: T 404 ARG cc_start: 0.5921 (OUTLIER) cc_final: 0.5500 (ppt170) REVERT: U 33 ASN cc_start: 0.8760 (m-40) cc_final: 0.8525 (m110) REVERT: U 94 GLN cc_start: 0.8500 (tt0) cc_final: 0.8273 (tm-30) REVERT: U 185 THR cc_start: 0.8936 (p) cc_final: 0.8658 (p) REVERT: U 188 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: V 143 MET cc_start: 0.8454 (ttp) cc_final: 0.8123 (mmp) REVERT: V 201 MET cc_start: 0.8688 (mtt) cc_final: 0.8432 (mtm) REVERT: W 61 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7494 (mmt90) REVERT: W 82 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: W 87 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8346 (ptm) REVERT: W 118 ARG cc_start: 0.8753 (ttp80) cc_final: 0.8416 (ttm110) REVERT: W 149 ASP cc_start: 0.8065 (m-30) cc_final: 0.7809 (m-30) REVERT: W 230 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6945 (mm-30) REVERT: X 6 TYR cc_start: 0.8996 (t80) cc_final: 0.8742 (t80) REVERT: X 17 LYS cc_start: 0.8799 (tttt) cc_final: 0.8525 (ttmm) REVERT: X 38 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8653 (mm-30) REVERT: X 78 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: X 191 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8420 (p) REVERT: Y 200 GLU cc_start: 0.8791 (pt0) cc_final: 0.8372 (pt0) REVERT: Z 131 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8425 (tpp) REVERT: Z 244 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8289 (mmtt) REVERT: Z 280 GLU cc_start: 0.8253 (pt0) cc_final: 0.7801 (pm20) REVERT: Z 281 LYS cc_start: 0.8666 (mttm) cc_final: 0.8315 (mtmt) REVERT: Z 287 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8483 (p) REVERT: a 198 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8480 (mttt) REVERT: a 242 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8145 (mm-30) REVERT: b 13 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8330 (mtpt) REVERT: b 68 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8400 (tp30) REVERT: b 106 MET cc_start: 0.8922 (mtt) cc_final: 0.8453 (mtt) REVERT: b 115 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7149 (tm-30) REVERT: b 151 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8065 (mm-30) outliers start: 172 outliers final: 111 residues processed: 1057 average time/residue: 1.4524 time to fit residues: 1886.6978 Evaluate side-chains 1086 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 939 time to evaluate : 4.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 402 LYS Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain J residue 12 MET Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 201 LYS Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain M residue 186 ARG Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 260 LEU Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 152 LYS Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 97 ASP Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 20 ILE Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 220 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 237 LYS Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 98 TYR Chi-restraints excluded: chain R residue 172 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 223 GLN Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 365 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 51 GLU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 188 GLU Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 241 GLN Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 230 GLU Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain X residue 201 LYS Chi-restraints excluded: chain Y residue 11 LYS Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 152 GLN Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain Z residue 287 SER Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 198 LYS Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 13 LYS Chi-restraints excluded: chain b residue 68 GLU Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 151 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 388 optimal weight: 0.9980 chunk 520 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 450 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 489 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 502 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 228 ASN B 19 GLN B 205 ASN D 18 GLN D 97 ASN D 143 HIS D 187 HIS ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 222 GLN ** L 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 228 ASN P 205 ASN R 223 GLN V 241 GLN W 86 ASN W 229 GLN Y 22 ASN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 222 GLN Z 291 GLN a 130 GLN b 105 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.109574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.092003 restraints weight = 62824.297| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.34 r_work: 0.2821 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 50122 Z= 0.320 Angle : 0.569 10.827 67810 Z= 0.300 Chirality : 0.044 0.230 7544 Planarity : 0.004 0.049 8790 Dihedral : 6.787 89.084 7085 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.03 % Favored : 97.90 % Rotamer: Outliers : 3.25 % Allowed : 24.05 % Favored : 72.70 % 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: 1.05 (0.10), residues: 6290 helix: 2.10 (0.10), residues: 2358 sheet: -0.08 (0.12), residues: 1572 loop : -0.09 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Z 154 HIS 0.007 0.001 HIS D 187 PHE 0.017 0.002 PHE Z 260 TYR 0.027 0.002 TYR J 96 ARG 0.010 0.001 ARG U 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26493.79 seconds wall clock time: 450 minutes 36.72 seconds (27036.72 seconds total)