Starting phenix.real_space_refine on Thu Jan 23 01:28:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e8l_47724/01_2025/9e8l_47724.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e8l_47724/01_2025/9e8l_47724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e8l_47724/01_2025/9e8l_47724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e8l_47724/01_2025/9e8l_47724.map" model { file = "/net/cci-nas-00/data/ceres_data/9e8l_47724/01_2025/9e8l_47724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e8l_47724/01_2025/9e8l_47724.cif" } resolution = 3.59 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= 0.003 sd= 0.028 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 14 5.49 5 Mg 3 5.21 5 S 374 5.16 5 C 44501 2.51 5 N 12115 2.21 5 O 13384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 480 residue(s): 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 70392 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3144 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 22, 'TRANS': 378} Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2917 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 351} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3053 Classifications: {'peptide': 386} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 369} Chain: "D" Number of atoms: 2811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2811 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 336} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2932 Classifications: {'peptide': 368} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Chain: "F" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1820 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 230} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1717 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "I" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1895 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1704 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "K" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "U" Number of atoms: 6538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 839, 6538 Classifications: {'peptide': 839} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 29, 'TRANS': 809} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3525 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 18, 'TRANS': 420} Chain breaks: 1 Chain: "W" Number of atoms: 3570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3570 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 8, 'TRANS': 429} Chain: "X" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2994 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 10, 'TRANS': 367} Chain: "Y" Number of atoms: 3127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3127 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 371} Chain: "Z" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "a" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2995 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "b" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1458 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain: "c" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2153 Classifications: {'peptide': 272} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 261} Chain breaks: 2 Chain: "d" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2188 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain: "e" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 361 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain breaks: 1 Chain: "f" Number of atoms: 6511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 6511 Classifications: {'peptide': 842} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 811} Chain breaks: 1 Chain: "g" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 771 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "u" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1376 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "v" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY Z 30 " occ=0.66 ... (2 atoms not shown) pdb=" O GLY Z 30 " occ=0.66 Time building chain proxies: 29.38, per 1000 atoms: 0.42 Number of scatterers: 70392 At special positions: 0 Unit cell: (194.928, 217.984, 207.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 374 16.00 P 14 15.00 Mg 3 11.99 O 13384 8.00 N 12115 7.00 C 44501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 154 " distance=2.03 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 186 " distance=2.04 Simple disulfide: pdb=" SG CYS U 633 " - pdb=" SG CYS U 659 " distance=2.01 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: 13.65 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 501 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 115 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 113 " 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16850 Finding SS restraints... Secondary structure from input PDB file: 424 helices and 45 sheets defined 59.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.06 Creating SS restraints... Processing helix chain 'A' and resid 26 through 37 removed outlier: 4.034A pdb=" N GLY A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 64 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.760A pdb=" N TRP A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 90 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 180 through 192 removed outlier: 3.503A pdb=" N VAL A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 204 removed outlier: 4.167A pdb=" N PHE A 201 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.620A pdb=" N LEU A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 267 removed outlier: 3.897A pdb=" N LYS A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 293 through 307 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 347 through 362 removed outlier: 3.791A pdb=" N SER A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 377 removed outlier: 3.743A pdb=" N LEU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 400 Processing helix chain 'A' and resid 405 through 422 Processing helix chain 'B' and resid 58 through 81 Processing helix chain 'B' and resid 92 through 103 removed outlier: 4.542A pdb=" N ASP B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 201 through 207 Processing helix chain 'B' and resid 208 through 215 Processing helix chain 'B' and resid 231 through 243 Processing helix chain 'B' and resid 253 through 256 Processing helix chain 'B' and resid 261 through 278 Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 304 through 318 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 357 through 371 removed outlier: 4.417A pdb=" N ARG B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 385 removed outlier: 3.565A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 409 Processing helix chain 'B' and resid 415 through 429 Processing helix chain 'C' and resid 22 through 67 removed outlier: 3.558A pdb=" N GLN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 154 through 171 Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 195 through 207 Processing helix chain 'C' and resid 215 through 220 removed outlier: 3.668A pdb=" N VAL C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 242 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 267 through 282 Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.059A pdb=" N LEU C 305 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 334 Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.819A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 373 Processing helix chain 'C' and resid 379 through 391 removed outlier: 3.578A pdb=" N ALA C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS C 389 " --> pdb=" O MET C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'D' and resid 40 through 83 Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 170 through 181 Processing helix chain 'D' and resid 181 through 187 Processing helix chain 'D' and resid 187 through 195 removed outlier: 3.713A pdb=" N TYR D 191 " --> pdb=" O HIS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 223 Processing helix chain 'D' and resid 244 through 256 Processing helix chain 'D' and resid 267 through 272 Processing helix chain 'D' and resid 279 through 299 Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.766A pdb=" N LEU D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 removed outlier: 3.711A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 4.362A pdb=" N TYR D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 389 Processing helix chain 'D' and resid 395 through 406 Processing helix chain 'E' and resid 16 through 51 Processing helix chain 'E' and resid 116 through 122 Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 150 through 155 Processing helix chain 'E' and resid 155 through 163 removed outlier: 3.964A pdb=" N PHE E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 191 Processing helix chain 'E' and resid 201 through 204 Processing helix chain 'E' and resid 209 through 225 Processing helix chain 'E' and resid 235 through 240 Processing helix chain 'E' and resid 251 through 266 removed outlier: 3.530A pdb=" N GLU E 259 " --> pdb=" O ARG E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 285 Processing helix chain 'E' and resid 286 through 291 removed outlier: 4.117A pdb=" N LEU E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 318 Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 339 through 358 Processing helix chain 'E' and resid 363 through 381 removed outlier: 3.651A pdb=" N LEU E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 56 Processing helix chain 'F' and resid 57 through 83 Processing helix chain 'F' and resid 169 through 176 removed outlier: 3.678A pdb=" N GLU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'F' and resid 191 through 208 removed outlier: 3.931A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 209 through 214 Processing helix chain 'F' and resid 232 through 244 removed outlier: 3.509A pdb=" N THR F 244 " --> pdb=" O CYS F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 258 removed outlier: 3.783A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLN F 258 " --> pdb=" O PRO F 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 253 through 258' Processing helix chain 'F' and resid 262 through 278 Processing helix chain 'F' and resid 288 through 293 removed outlier: 3.713A pdb=" N THR F 293 " --> pdb=" O ASP F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 316 removed outlier: 3.695A pdb=" N ASN F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 339 removed outlier: 4.191A pdb=" N LEU F 338 " --> pdb=" O ARG F 334 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP F 339 " --> pdb=" O VAL F 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 334 through 339' Processing helix chain 'F' and resid 358 through 371 Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing helix chain 'F' and resid 380 through 388 removed outlier: 3.531A pdb=" N LEU F 384 " --> pdb=" O ASN F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 411 Processing helix chain 'F' and resid 416 through 428 Processing helix chain 'G' and resid 22 through 32 removed outlier: 3.573A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA G 31 " --> pdb=" O TYR G 27 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 128 Processing helix chain 'G' and resid 171 through 184 Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 231 through 244 Processing helix chain 'H' and resid 19 through 29 removed outlier: 3.597A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 102 removed outlier: 3.850A pdb=" N TYR H 83 " --> pdb=" O MET H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 122 removed outlier: 3.668A pdb=" N THR H 122 " --> pdb=" O MET H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 177 Processing helix chain 'H' and resid 183 through 199 Processing helix chain 'H' and resid 222 through 231 Processing helix chain 'I' and resid 4 through 8 removed outlier: 3.707A pdb=" N ARG I 8 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 30 removed outlier: 3.821A pdb=" N HIS I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 102 Processing helix chain 'I' and resid 106 through 124 removed outlier: 3.647A pdb=" N PHE I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 178 Processing helix chain 'I' and resid 185 through 201 Processing helix chain 'I' and resid 219 through 222 Processing helix chain 'I' and resid 229 through 250 removed outlier: 3.556A pdb=" N VAL I 233 " --> pdb=" O LYS I 229 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU I 250 " --> pdb=" O LYS I 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 28 Processing helix chain 'J' and resid 55 through 60 removed outlier: 3.521A pdb=" N VAL J 59 " --> pdb=" O GLU J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 98 Processing helix chain 'J' and resid 103 through 120 Processing helix chain 'J' and resid 164 through 176 Processing helix chain 'J' and resid 183 through 197 removed outlier: 3.873A pdb=" N THR J 187 " --> pdb=" O THR J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 238 removed outlier: 3.512A pdb=" N TYR J 228 " --> pdb=" O GLU J 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 33 removed outlier: 3.533A pdb=" N ALA K 27 " --> pdb=" O GLN K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 64 removed outlier: 3.794A pdb=" N ILE K 64 " --> pdb=" O PRO K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 104 Processing helix chain 'K' and resid 108 through 121 Processing helix chain 'K' and resid 173 through 185 Processing helix chain 'K' and resid 190 through 206 Processing helix chain 'K' and resid 234 through 241 Processing helix chain 'L' and resid 19 through 32 removed outlier: 3.512A pdb=" N GLU L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 100 Processing helix chain 'L' and resid 104 through 118 removed outlier: 4.045A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 122 Processing helix chain 'L' and resid 164 through 180 removed outlier: 4.657A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 199 removed outlier: 3.575A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU L 199 " --> pdb=" O LEU L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 234 Proline residue: L 231 - end of helix Processing helix chain 'M' and resid 22 through 32 removed outlier: 3.783A pdb=" N LYS M 28 " --> pdb=" O GLU M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 103 removed outlier: 3.538A pdb=" N GLY M 103 " --> pdb=" O ARG M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 125 removed outlier: 3.764A pdb=" N LEU M 124 " --> pdb=" O HIS M 120 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 177 Processing helix chain 'M' and resid 185 through 200 removed outlier: 4.042A pdb=" N ILE M 189 " --> pdb=" O THR M 185 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 242 Processing helix chain 'U' and resid 6 through 8 No H-bonds generated for 'chain 'U' and resid 6 through 8' Processing helix chain 'U' and resid 9 through 14 Processing helix chain 'U' and resid 16 through 29 removed outlier: 3.724A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 40 removed outlier: 9.189A pdb=" N ALA U 36 " --> pdb=" O ASN U 32 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU U 37 " --> pdb=" O ASP U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 51 removed outlier: 5.870A pdb=" N LEU U 48 " --> pdb=" O LYS U 44 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR U 49 " --> pdb=" O ILE U 45 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU U 50 " --> pdb=" O GLU U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 removed outlier: 3.597A pdb=" N ALA U 60 " --> pdb=" O SER U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 83 removed outlier: 3.805A pdb=" N GLY U 83 " --> pdb=" O ASN U 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 89 removed outlier: 5.935A pdb=" N LEU U 87 " --> pdb=" O ALA U 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 117 removed outlier: 4.868A pdb=" N ASP U 106 " --> pdb=" O ALA U 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP U 117 " --> pdb=" O VAL U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 142 Processing helix chain 'U' and resid 149 through 157 removed outlier: 3.815A pdb=" N ILE U 153 " --> pdb=" O GLN U 149 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU U 155 " --> pdb=" O ILE U 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 169 removed outlier: 4.289A pdb=" N ILE U 167 " --> pdb=" O PHE U 163 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU U 168 " --> pdb=" O GLU U 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 187 removed outlier: 4.093A pdb=" N LEU U 177 " --> pdb=" O VAL U 173 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU U 181 " --> pdb=" O LEU U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 190 through 206 removed outlier: 4.821A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 224 removed outlier: 3.630A pdb=" N CYS U 217 " --> pdb=" O PHE U 213 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN U 218 " --> pdb=" O ILE U 214 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N CYS U 219 " --> pdb=" O ASN U 215 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU U 220 " --> pdb=" O VAL U 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 239 Processing helix chain 'U' and resid 242 through 254 Processing helix chain 'U' and resid 257 through 270 removed outlier: 4.114A pdb=" N SER U 263 " --> pdb=" O GLN U 259 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL U 264 " --> pdb=" O PHE U 260 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN U 266 " --> pdb=" O SER U 262 " (cutoff:3.500A) Processing helix chain 'U' and resid 321 through 330 removed outlier: 3.763A pdb=" N MET U 325 " --> pdb=" O GLN U 321 " (cutoff:3.500A) Processing helix chain 'U' and resid 335 through 345 Processing helix chain 'U' and resid 350 through 355 Processing helix chain 'U' and resid 364 through 377 removed outlier: 3.857A pdb=" N VAL U 370 " --> pdb=" O HIS U 366 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE U 371 " --> pdb=" O THR U 367 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER U 374 " --> pdb=" O VAL U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 389 removed outlier: 3.691A pdb=" N ASN U 389 " --> pdb=" O PHE U 385 " (cutoff:3.500A) Processing helix chain 'U' and resid 390 through 395 Processing helix chain 'U' and resid 398 through 412 removed outlier: 3.520A pdb=" N PHE U 402 " --> pdb=" O ASN U 398 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU U 408 " --> pdb=" O ALA U 404 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL U 410 " --> pdb=" O ALA U 406 " (cutoff:3.500A) Processing helix chain 'U' and resid 418 through 427 removed outlier: 4.196A pdb=" N ALA U 424 " --> pdb=" O LEU U 420 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 450 removed outlier: 3.829A pdb=" N GLY U 447 " --> pdb=" O LEU U 443 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS U 450 " --> pdb=" O LEU U 446 " (cutoff:3.500A) Processing helix chain 'U' and resid 456 through 465 removed outlier: 3.631A pdb=" N TYR U 460 " --> pdb=" O ASP U 456 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 485 Processing helix chain 'U' and resid 490 through 502 Processing helix chain 'U' and resid 505 through 519 removed outlier: 3.606A pdb=" N LEU U 514 " --> pdb=" O GLU U 510 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY U 517 " --> pdb=" O GLY U 513 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 537 Processing helix chain 'U' and resid 541 through 555 removed outlier: 4.027A pdb=" N VAL U 550 " --> pdb=" O ARG U 546 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA U 553 " --> pdb=" O ALA U 549 " (cutoff:3.500A) Processing helix chain 'U' and resid 559 through 562 Processing helix chain 'U' and resid 563 through 571 removed outlier: 3.863A pdb=" N SER U 569 " --> pdb=" O ALA U 565 " (cutoff:3.500A) Processing helix chain 'U' and resid 575 through 590 removed outlier: 3.742A pdb=" N TYR U 590 " --> pdb=" O VAL U 586 " (cutoff:3.500A) Processing helix chain 'U' and resid 595 through 609 removed outlier: 3.987A pdb=" N HIS U 604 " --> pdb=" O ARG U 600 " (cutoff:3.500A) Processing helix chain 'U' and resid 611 through 621 Processing helix chain 'U' and resid 622 through 627 removed outlier: 3.669A pdb=" N PHE U 627 " --> pdb=" O GLY U 623 " (cutoff:3.500A) Processing helix chain 'U' and resid 631 through 641 removed outlier: 4.164A pdb=" N SER U 635 " --> pdb=" O GLU U 631 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 660 Processing helix chain 'U' and resid 666 through 676 Proline residue: U 674 - end of helix Processing helix chain 'U' and resid 680 through 696 removed outlier: 3.537A pdb=" N ILE U 694 " --> pdb=" O ALA U 690 " (cutoff:3.500A) Processing helix chain 'U' and resid 705 through 719 removed outlier: 4.177A pdb=" N LYS U 715 " --> pdb=" O GLN U 711 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN U 718 " --> pdb=" O SER U 714 " (cutoff:3.500A) Processing helix chain 'U' and resid 723 through 738 Processing helix chain 'U' and resid 756 through 768 removed outlier: 3.742A pdb=" N GLN U 768 " --> pdb=" O LEU U 764 " (cutoff:3.500A) Processing helix chain 'U' and resid 769 through 771 No H-bonds generated for 'chain 'U' and resid 769 through 771' Processing helix chain 'U' and resid 772 through 781 removed outlier: 3.977A pdb=" N HIS U 777 " --> pdb=" O PRO U 774 " (cutoff:3.500A) Processing helix chain 'U' and resid 835 through 844 Processing helix chain 'U' and resid 885 through 891 removed outlier: 4.445A pdb=" N LYS U 890 " --> pdb=" O ALA U 887 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 35 removed outlier: 3.763A pdb=" N ASP V 34 " --> pdb=" O PRO V 30 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL V 35 " --> pdb=" O ALA V 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 30 through 35' Processing helix chain 'V' and resid 35 through 51 removed outlier: 4.002A pdb=" N ALA V 41 " --> pdb=" O MET V 37 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 67 Processing helix chain 'V' and resid 67 through 72 Processing helix chain 'V' and resid 88 through 93 Processing helix chain 'V' and resid 132 through 140 removed outlier: 4.817A pdb=" N GLU V 137 " --> pdb=" O PRO V 133 " (cutoff:3.500A) Proline residue: V 138 - end of helix Processing helix chain 'V' and resid 147 through 157 removed outlier: 3.889A pdb=" N ALA V 155 " --> pdb=" O THR V 151 " (cutoff:3.500A) Processing helix chain 'V' and resid 160 through 165 Processing helix chain 'V' and resid 170 through 192 removed outlier: 4.379A pdb=" N ARG V 180 " --> pdb=" O MET V 176 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS V 182 " --> pdb=" O SER V 178 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU V 191 " --> pdb=" O ILE V 187 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET V 192 " --> pdb=" O SER V 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 198 through 221 removed outlier: 3.673A pdb=" N ALA V 202 " --> pdb=" O GLN V 198 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU V 205 " --> pdb=" O ARG V 201 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL V 206 " --> pdb=" O ALA V 202 " (cutoff:3.500A) Processing helix chain 'V' and resid 224 through 240 removed outlier: 3.538A pdb=" N ARG V 228 " --> pdb=" O LEU V 224 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE V 230 " --> pdb=" O VAL V 226 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA V 233 " --> pdb=" O SER V 229 " (cutoff:3.500A) Processing helix chain 'V' and resid 245 through 262 removed outlier: 3.668A pdb=" N THR V 249 " --> pdb=" O ASP V 245 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR V 258 " --> pdb=" O LEU V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 266 through 270 removed outlier: 3.849A pdb=" N LYS V 269 " --> pdb=" O GLN V 266 " (cutoff:3.500A) Processing helix chain 'V' and resid 282 through 299 removed outlier: 4.331A pdb=" N ARG V 287 " --> pdb=" O ASN V 283 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE V 298 " --> pdb=" O ARG V 294 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 314 removed outlier: 4.045A pdb=" N ARG V 314 " --> pdb=" O THR V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 321 through 339 removed outlier: 3.644A pdb=" N LEU V 331 " --> pdb=" O THR V 327 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL V 334 " --> pdb=" O LYS V 330 " (cutoff:3.500A) Processing helix chain 'V' and resid 344 through 349 Processing helix chain 'V' and resid 350 through 352 No H-bonds generated for 'chain 'V' and resid 350 through 352' Processing helix chain 'V' and resid 353 through 368 Proline residue: V 359 - end of helix Processing helix chain 'V' and resid 371 through 380 removed outlier: 3.648A pdb=" N PHE V 375 " --> pdb=" O ASN V 371 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL V 378 " --> pdb=" O LYS V 374 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP V 380 " --> pdb=" O ASN V 376 " (cutoff:3.500A) Processing helix chain 'V' and resid 382 through 389 Processing helix chain 'V' and resid 391 through 398 removed outlier: 4.152A pdb=" N LEU V 398 " --> pdb=" O ILE V 395 " (cutoff:3.500A) Processing helix chain 'V' and resid 402 through 413 removed outlier: 4.300A pdb=" N GLY V 406 " --> pdb=" O VAL V 402 " (cutoff:3.500A) Processing helix chain 'V' and resid 420 through 425 removed outlier: 3.691A pdb=" N LYS V 425 " --> pdb=" O ASP V 421 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 445 removed outlier: 5.059A pdb=" N PHE V 436 " --> pdb=" O GLU V 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 453 through 455 No H-bonds generated for 'chain 'V' and resid 453 through 455' Processing helix chain 'V' and resid 470 through 493 removed outlier: 3.723A pdb=" N ARG V 479 " --> pdb=" O ALA V 475 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 25 removed outlier: 3.904A pdb=" N VAL W 24 " --> pdb=" O TYR W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 37 removed outlier: 3.612A pdb=" N LYS W 33 " --> pdb=" O PRO W 29 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS W 36 " --> pdb=" O ALA W 32 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU W 37 " --> pdb=" O LYS W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 53 removed outlier: 4.489A pdb=" N LYS W 52 " --> pdb=" O LEU W 48 " (cutoff:3.500A) Processing helix chain 'W' and resid 54 through 58 removed outlier: 3.551A pdb=" N ALA W 57 " --> pdb=" O THR W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 76 removed outlier: 4.200A pdb=" N ARG W 65 " --> pdb=" O VAL W 61 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL W 68 " --> pdb=" O SER W 64 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET W 73 " --> pdb=" O ALA W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 92 removed outlier: 3.563A pdb=" N GLU W 85 " --> pdb=" O ASP W 81 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN W 86 " --> pdb=" O LEU W 82 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU W 90 " --> pdb=" O ASN W 86 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS W 92 " --> pdb=" O MET W 88 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 114 removed outlier: 3.515A pdb=" N GLN W 107 " --> pdb=" O LYS W 103 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR W 110 " --> pdb=" O GLN W 106 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR W 111 " --> pdb=" O GLN W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 132 removed outlier: 3.801A pdb=" N LEU W 124 " --> pdb=" O ILE W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 135 through 137 No H-bonds generated for 'chain 'W' and resid 135 through 137' Processing helix chain 'W' and resid 138 through 157 Processing helix chain 'W' and resid 158 through 169 removed outlier: 3.722A pdb=" N SER W 164 " --> pdb=" O LYS W 160 " (cutoff:3.500A) Processing helix chain 'W' and resid 170 through 174 Processing helix chain 'W' and resid 180 through 196 removed outlier: 4.694A pdb=" N ILE W 186 " --> pdb=" O ARG W 182 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU W 187 " --> pdb=" O VAL W 183 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU W 188 " --> pdb=" O GLU W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 207 Processing helix chain 'W' and resid 208 through 209 No H-bonds generated for 'chain 'W' and resid 208 through 209' Processing helix chain 'W' and resid 210 through 216 Processing helix chain 'W' and resid 219 through 238 removed outlier: 4.090A pdb=" N GLN W 232 " --> pdb=" O ASN W 228 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 252 removed outlier: 3.789A pdb=" N LYS W 245 " --> pdb=" O LEU W 241 " (cutoff:3.500A) Processing helix chain 'W' and resid 253 through 258 removed outlier: 3.554A pdb=" N ALA W 258 " --> pdb=" O PRO W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 259 through 277 Processing helix chain 'W' and resid 280 through 292 removed outlier: 3.640A pdb=" N GLY W 292 " --> pdb=" O HIS W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 298 Processing helix chain 'W' and resid 299 through 311 removed outlier: 4.022A pdb=" N LEU W 305 " --> pdb=" O LYS W 301 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 330 removed outlier: 6.071A pdb=" N MET W 326 " --> pdb=" O GLU W 322 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU W 327 " --> pdb=" O ASP W 323 " (cutoff:3.500A) Processing helix chain 'W' and resid 338 through 342 removed outlier: 3.808A pdb=" N PHE W 341 " --> pdb=" O THR W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 344 through 369 Processing helix chain 'W' and resid 375 through 383 Processing helix chain 'W' and resid 385 through 399 Processing helix chain 'W' and resid 420 through 452 removed outlier: 3.642A pdb=" N ILE W 452 " --> pdb=" O LYS W 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 45 through 60 removed outlier: 3.696A pdb=" N SER X 55 " --> pdb=" O LEU X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 61 through 64 removed outlier: 3.968A pdb=" N ALA X 64 " --> pdb=" O GLY X 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 61 through 64' Processing helix chain 'X' and resid 65 through 73 removed outlier: 3.543A pdb=" N LEU X 69 " --> pdb=" O GLU X 65 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LYS X 71 " --> pdb=" O GLY X 67 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 80 Processing helix chain 'X' and resid 81 through 98 Processing helix chain 'X' and resid 107 through 120 Processing helix chain 'X' and resid 122 through 140 Processing helix chain 'X' and resid 142 through 160 Processing helix chain 'X' and resid 162 through 180 removed outlier: 4.412A pdb=" N GLU X 168 " --> pdb=" O ALA X 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 198 Processing helix chain 'X' and resid 203 through 221 Processing helix chain 'X' and resid 225 through 241 Processing helix chain 'X' and resid 242 through 243 No H-bonds generated for 'chain 'X' and resid 242 through 243' Processing helix chain 'X' and resid 244 through 245 No H-bonds generated for 'chain 'X' and resid 244 through 245' Processing helix chain 'X' and resid 246 through 261 Processing helix chain 'X' and resid 264 through 272 removed outlier: 3.863A pdb=" N GLN X 268 " --> pdb=" O PRO X 264 " (cutoff:3.500A) Processing helix chain 'X' and resid 275 through 280 Processing helix chain 'X' and resid 281 through 296 removed outlier: 3.773A pdb=" N LEU X 287 " --> pdb=" O GLN X 283 " (cutoff:3.500A) Processing helix chain 'X' and resid 298 through 309 Processing helix chain 'X' and resid 309 through 314 Processing helix chain 'X' and resid 316 through 340 removed outlier: 4.051A pdb=" N GLU X 340 " --> pdb=" O ILE X 336 " (cutoff:3.500A) Processing helix chain 'X' and resid 347 through 355 Processing helix chain 'X' and resid 357 through 371 removed outlier: 4.359A pdb=" N ARG X 363 " --> pdb=" O ALA X 359 " (cutoff:3.500A) Processing helix chain 'X' and resid 394 through 417 removed outlier: 3.829A pdb=" N GLU X 398 " --> pdb=" O ASP X 394 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 28 through 33 Processing helix chain 'Y' and resid 37 through 48 removed outlier: 3.805A pdb=" N MET Y 42 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA Y 43 " --> pdb=" O ASP Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 58 Processing helix chain 'Y' and resid 66 through 95 Processing helix chain 'Y' and resid 96 through 114 Processing helix chain 'Y' and resid 116 through 130 Processing helix chain 'Y' and resid 133 through 152 removed outlier: 3.571A pdb=" N LEU Y 138 " --> pdb=" O LEU Y 134 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP Y 139 " --> pdb=" O GLY Y 135 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE Y 140 " --> pdb=" O HIS Y 136 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL Y 141 " --> pdb=" O ARG Y 137 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 169 Processing helix chain 'Y' and resid 173 through 191 removed outlier: 3.865A pdb=" N LYS Y 181 " --> pdb=" O ARG Y 177 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL Y 182 " --> pdb=" O ASN Y 178 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 204 removed outlier: 3.567A pdb=" N GLU Y 199 " --> pdb=" O LYS Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 231 removed outlier: 3.550A pdb=" N MET Y 228 " --> pdb=" O VAL Y 224 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 240 Processing helix chain 'Y' and resid 243 through 251 Processing helix chain 'Y' and resid 253 through 265 removed outlier: 3.805A pdb=" N TYR Y 259 " --> pdb=" O ALA Y 255 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU Y 263 " --> pdb=" O TYR Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 267 through 285 removed outlier: 4.191A pdb=" N GLN Y 280 " --> pdb=" O ALA Y 276 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU Y 281 " --> pdb=" O VAL Y 277 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 290 No H-bonds generated for 'chain 'Y' and resid 288 through 290' Processing helix chain 'Y' and resid 291 through 308 Processing helix chain 'Y' and resid 316 through 324 Processing helix chain 'Y' and resid 326 through 340 removed outlier: 3.550A pdb=" N ILE Y 330 " --> pdb=" O GLY Y 326 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 384 removed outlier: 4.257A pdb=" N ARG Y 379 " --> pdb=" O LEU Y 375 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 28 removed outlier: 3.822A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'Z' and resid 104 through 114 removed outlier: 3.706A pdb=" N ILE Z 108 " --> pdb=" O ASN Z 104 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) Processing helix chain 'Z' and resid 165 through 178 removed outlier: 3.550A pdb=" N LEU Z 175 " --> pdb=" O GLY Z 171 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP Z 178 " --> pdb=" O HIS Z 174 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 217 Processing helix chain 'Z' and resid 226 through 237 removed outlier: 3.561A pdb=" N LEU Z 237 " --> pdb=" O VAL Z 233 " (cutoff:3.500A) Processing helix chain 'Z' and resid 242 through 290 removed outlier: 3.589A pdb=" N ASN Z 277 " --> pdb=" O HIS Z 273 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY Z 290 " --> pdb=" O GLU Z 286 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 11 Processing helix chain 'a' and resid 17 through 31 removed outlier: 4.749A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU a 25 " --> pdb=" O VAL a 21 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU a 28 " --> pdb=" O ARG a 24 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS a 31 " --> pdb=" O GLU a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 44 removed outlier: 3.790A pdb=" N LEU a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN a 40 " --> pdb=" O GLN a 36 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU a 42 " --> pdb=" O THR a 38 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP a 43 " --> pdb=" O LEU a 39 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE a 44 " --> pdb=" O GLN a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 47 No H-bonds generated for 'chain 'a' and resid 45 through 47' Processing helix chain 'a' and resid 52 through 64 removed outlier: 4.034A pdb=" N LEU a 56 " --> pdb=" O GLN a 52 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASN a 62 " --> pdb=" O LYS a 58 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 87 removed outlier: 5.578A pdb=" N ILE a 79 " --> pdb=" O SER a 75 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG a 85 " --> pdb=" O LEU a 81 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 102 removed outlier: 4.111A pdb=" N LEU a 94 " --> pdb=" O PRO a 90 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU a 98 " --> pdb=" O LEU a 94 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS a 99 " --> pdb=" O THR a 95 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR a 100 " --> pdb=" O PHE a 96 " (cutoff:3.500A) Processing helix chain 'a' and resid 110 through 125 removed outlier: 3.631A pdb=" N CYS a 114 " --> pdb=" O ALA a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 132 through 140 removed outlier: 5.118A pdb=" N VAL a 138 " --> pdb=" O THR a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 148 removed outlier: 4.055A pdb=" N VAL a 148 " --> pdb=" O LEU a 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 145 through 148' Processing helix chain 'a' and resid 149 through 162 Processing helix chain 'a' and resid 163 through 165 No H-bonds generated for 'chain 'a' and resid 163 through 165' Processing helix chain 'a' and resid 169 through 183 removed outlier: 3.530A pdb=" N VAL a 183 " --> pdb=" O PHE a 179 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 207 Processing helix chain 'a' and resid 215 through 218 Processing helix chain 'a' and resid 219 through 227 removed outlier: 3.788A pdb=" N GLU a 223 " --> pdb=" O HIS a 219 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER a 224 " --> pdb=" O PRO a 220 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU a 225 " --> pdb=" O VAL a 221 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG a 226 " --> pdb=" O LEU a 222 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 241 Processing helix chain 'a' and resid 247 through 257 Processing helix chain 'a' and resid 261 through 263 No H-bonds generated for 'chain 'a' and resid 261 through 263' Processing helix chain 'a' and resid 264 through 283 Processing helix chain 'a' and resid 292 through 300 Processing helix chain 'a' and resid 305 through 318 removed outlier: 4.539A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 371 removed outlier: 3.543A pdb=" N TRP a 356 " --> pdb=" O ARG a 352 " (cutoff:3.500A) Processing helix chain 'a' and resid 371 through 376 Processing helix chain 'b' and resid 13 through 18 Processing helix chain 'b' and resid 24 through 43 removed outlier: 3.959A pdb=" N GLN b 30 " --> pdb=" O LEU b 26 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP b 31 " --> pdb=" O GLN b 27 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER b 39 " --> pdb=" O ILE b 35 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS b 40 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER b 43 " --> pdb=" O SER b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 74 removed outlier: 3.858A pdb=" N ILE b 71 " --> pdb=" O ASP b 67 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 99 removed outlier: 5.146A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS b 94 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS b 99 " --> pdb=" O LEU b 95 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 134 removed outlier: 3.636A pdb=" N ALA b 128 " --> pdb=" O LEU b 124 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS b 129 " --> pdb=" O VAL b 125 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 161 Processing helix chain 'b' and resid 180 through 185 Processing helix chain 'c' and resid 34 through 49 removed outlier: 3.509A pdb=" N VAL c 49 " --> pdb=" O GLY c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 87 Processing helix chain 'c' and resid 88 through 103 Processing helix chain 'c' and resid 123 through 137 Processing helix chain 'c' and resid 188 through 195 Processing helix chain 'c' and resid 212 through 217 removed outlier: 3.816A pdb=" N MET c 216 " --> pdb=" O LEU c 212 " (cutoff:3.500A) Processing helix chain 'c' and resid 218 through 221 Processing helix chain 'c' and resid 224 through 230 Processing helix chain 'c' and resid 233 through 260 removed outlier: 3.531A pdb=" N LYS c 246 " --> pdb=" O GLU c 242 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN c 254 " --> pdb=" O GLU c 250 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS c 257 " --> pdb=" O LYS c 253 " (cutoff:3.500A) Processing helix chain 'c' and resid 279 through 309 removed outlier: 3.689A pdb=" N HIS c 283 " --> pdb=" O ASP c 279 " (cutoff:3.500A) Processing helix chain 'd' and resid 83 through 104 Processing helix chain 'd' and resid 108 through 123 removed outlier: 3.780A pdb=" N LEU d 121 " --> pdb=" O GLY d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 138 through 159 removed outlier: 3.523A pdb=" N LEU d 157 " --> pdb=" O GLN d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 177 removed outlier: 3.697A pdb=" N GLN d 170 " --> pdb=" O ARG d 166 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N CYS d 173 " --> pdb=" O ALA d 169 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR d 174 " --> pdb=" O GLN d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 202 Processing helix chain 'd' and resid 204 through 215 removed outlier: 3.663A pdb=" N LEU d 212 " --> pdb=" O PHE d 208 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU d 213 " --> pdb=" O HIS d 209 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG d 214 " --> pdb=" O THR d 210 " (cutoff:3.500A) Processing helix chain 'd' and resid 216 through 223 Processing helix chain 'd' and resid 223 through 238 Proline residue: d 229 - end of helix Processing helix chain 'd' and resid 240 through 245 Processing helix chain 'd' and resid 253 through 279 removed outlier: 3.888A pdb=" N ASP d 265 " --> pdb=" O ASP d 261 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU d 276 " --> pdb=" O ALA d 272 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS d 277 " --> pdb=" O GLY d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 284 through 291 removed outlier: 4.173A pdb=" N ARG d 289 " --> pdb=" O THR d 285 " (cutoff:3.500A) Processing helix chain 'd' and resid 296 through 307 removed outlier: 4.015A pdb=" N THR d 300 " --> pdb=" O PRO d 296 " (cutoff:3.500A) Processing helix chain 'd' and resid 318 through 323 removed outlier: 3.732A pdb=" N GLN d 322 " --> pdb=" O PHE d 318 " (cutoff:3.500A) Processing helix chain 'd' and resid 332 through 348 Processing helix chain 'e' and resid 42 through 47 removed outlier: 3.560A pdb=" N ASP e 46 " --> pdb=" O TRP e 43 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN e 47 " --> pdb=" O ASP e 44 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 62 Processing helix chain 'f' and resid 46 through 62 removed outlier: 3.628A pdb=" N VAL f 60 " --> pdb=" O LEU f 56 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 72 removed outlier: 3.661A pdb=" N TYR f 71 " --> pdb=" O ASP f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 72 through 88 Processing helix chain 'f' and resid 93 through 99 removed outlier: 3.512A pdb=" N PHE f 98 " --> pdb=" O LYS f 94 " (cutoff:3.500A) Processing helix chain 'f' and resid 106 through 113 removed outlier: 3.707A pdb=" N TYR f 110 " --> pdb=" O LEU f 106 " (cutoff:3.500A) Processing helix chain 'f' and resid 116 through 131 removed outlier: 3.740A pdb=" N MET f 131 " --> pdb=" O SER f 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 135 through 146 removed outlier: 4.465A pdb=" N LEU f 140 " --> pdb=" O GLU f 136 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS f 141 " --> pdb=" O ARG f 137 " (cutoff:3.500A) Processing helix chain 'f' and resid 150 through 154 Processing helix chain 'f' and resid 155 through 173 removed outlier: 4.318A pdb=" N GLN f 171 " --> pdb=" O ALA f 167 " (cutoff:3.500A) Processing helix chain 'f' and resid 180 through 198 removed outlier: 3.718A pdb=" N LEU f 184 " --> pdb=" O GLN f 180 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU f 187 " --> pdb=" O PRO f 183 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU f 190 " --> pdb=" O THR f 186 " (cutoff:3.500A) Proline residue: f 193 - end of helix Processing helix chain 'f' and resid 200 through 211 Processing helix chain 'f' and resid 213 through 218 removed outlier: 3.629A pdb=" N MET f 216 " --> pdb=" O GLN f 213 " (cutoff:3.500A) Processing helix chain 'f' and resid 225 through 237 removed outlier: 3.932A pdb=" N VAL f 229 " --> pdb=" O ALA f 225 " (cutoff:3.500A) Processing helix chain 'f' and resid 243 through 259 Processing helix chain 'f' and resid 261 through 272 Processing helix chain 'f' and resid 274 through 285 removed outlier: 3.726A pdb=" N ILE f 281 " --> pdb=" O LEU f 277 " (cutoff:3.500A) Processing helix chain 'f' and resid 287 through 302 Processing helix chain 'f' and resid 313 through 323 Processing helix chain 'f' and resid 325 through 337 Processing helix chain 'f' and resid 344 through 350 Processing helix chain 'f' and resid 367 through 382 Processing helix chain 'f' and resid 394 through 400 removed outlier: 3.695A pdb=" N LEU f 399 " --> pdb=" O GLY f 395 " (cutoff:3.500A) Processing helix chain 'f' and resid 401 through 403 No H-bonds generated for 'chain 'f' and resid 401 through 403' Processing helix chain 'f' and resid 404 through 418 removed outlier: 3.903A pdb=" N LEU f 408 " --> pdb=" O ASP f 404 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA f 412 " --> pdb=" O LEU f 408 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU f 414 " --> pdb=" O ALA f 410 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY f 415 " --> pdb=" O ALA f 411 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET f 416 " --> pdb=" O ALA f 412 " (cutoff:3.500A) Processing helix chain 'f' and resid 421 through 426 Processing helix chain 'f' and resid 429 through 434 Processing helix chain 'f' and resid 438 through 451 removed outlier: 3.786A pdb=" N LEU f 446 " --> pdb=" O SER f 442 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY f 449 " --> pdb=" O LEU f 445 " (cutoff:3.500A) Processing helix chain 'f' and resid 460 through 467 Processing helix chain 'f' and resid 474 through 489 Processing helix chain 'f' and resid 494 through 502 Processing helix chain 'f' and resid 503 through 506 Processing helix chain 'f' and resid 511 through 526 Processing helix chain 'f' and resid 531 through 544 removed outlier: 3.750A pdb=" N THR f 537 " --> pdb=" O ASP f 533 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU f 544 " --> pdb=" O GLN f 540 " (cutoff:3.500A) Processing helix chain 'f' and resid 546 through 551 Processing helix chain 'f' and resid 554 through 556 No H-bonds generated for 'chain 'f' and resid 554 through 556' Processing helix chain 'f' and resid 557 through 564 Processing helix chain 'f' and resid 565 through 567 No H-bonds generated for 'chain 'f' and resid 565 through 567' Processing helix chain 'f' and resid 569 through 571 No H-bonds generated for 'chain 'f' and resid 569 through 571' Processing helix chain 'f' and resid 572 through 581 removed outlier: 4.010A pdb=" N ILE f 576 " --> pdb=" O ALA f 572 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA f 578 " --> pdb=" O GLU f 574 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA f 579 " --> pdb=" O ALA f 575 " (cutoff:3.500A) Processing helix chain 'f' and resid 586 through 600 Processing helix chain 'f' and resid 605 through 617 Processing helix chain 'f' and resid 644 through 646 No H-bonds generated for 'chain 'f' and resid 644 through 646' Processing helix chain 'f' and resid 647 through 662 removed outlier: 3.976A pdb=" N GLY f 651 " --> pdb=" O GLY f 647 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL f 652 " --> pdb=" O ALA f 648 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA f 653 " --> pdb=" O HIS f 649 " (cutoff:3.500A) Processing helix chain 'f' and resid 664 through 682 removed outlier: 3.959A pdb=" N ARG f 673 " --> pdb=" O GLU f 669 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY f 676 " --> pdb=" O LEU f 672 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N HIS f 677 " --> pdb=" O ARG f 673 " (cutoff:3.500A) Processing helix chain 'f' and resid 683 through 698 removed outlier: 3.693A pdb=" N ALA f 689 " --> pdb=" O THR f 685 " (cutoff:3.500A) Proline residue: f 691 - end of helix removed outlier: 3.512A pdb=" N LEU f 696 " --> pdb=" O LEU f 692 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER f 698 " --> pdb=" O LEU f 694 " (cutoff:3.500A) Processing helix chain 'f' and resid 703 through 715 removed outlier: 4.475A pdb=" N THR f 709 " --> pdb=" O ASN f 705 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS f 715 " --> pdb=" O SER f 711 " (cutoff:3.500A) Processing helix chain 'f' and resid 718 through 733 removed outlier: 3.705A pdb=" N GLY f 730 " --> pdb=" O ILE f 726 " (cutoff:3.500A) Processing helix chain 'f' and resid 738 through 752 Processing helix chain 'f' and resid 755 through 770 Processing helix chain 'f' and resid 771 through 774 removed outlier: 3.584A pdb=" N GLY f 774 " --> pdb=" O LEU f 771 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 771 through 774' Processing helix chain 'f' and resid 789 through 803 removed outlier: 4.069A pdb=" N VAL f 799 " --> pdb=" O GLY f 795 " (cutoff:3.500A) Processing helix chain 'f' and resid 804 through 806 No H-bonds generated for 'chain 'f' and resid 804 through 806' Processing helix chain 'f' and resid 814 through 825 Processing helix chain 'g' and resid 108 through 120 Processing helix chain 'g' and resid 161 through 170 removed outlier: 3.530A pdb=" N ARG g 166 " --> pdb=" O GLU g 162 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE g 169 " --> pdb=" O ALA g 165 " (cutoff:3.500A) Processing helix chain 'u' and resid 127 through 130 Processing helix chain 'u' and resid 145 through 150 removed outlier: 3.894A pdb=" N CYS u 149 " --> pdb=" O GLY u 145 " (cutoff:3.500A) Processing helix chain 'u' and resid 205 through 212 Processing helix chain 'u' and resid 221 through 226 Processing helix chain 'u' and resid 234 through 238 Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 123 removed outlier: 5.038A pdb=" N GLU B 130 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER B 124 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU B 112 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY B 161 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN B 153 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 159 " --> pdb=" O ASN B 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 152 removed outlier: 5.775A pdb=" N GLY A 141 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLU B 130 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER B 124 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU B 112 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS C 94 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU C 86 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 240 removed outlier: 6.094A pdb=" N CYS A 236 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE A 273 " --> pdb=" O CYS A 236 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE A 238 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS A 270 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU A 318 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 272 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ALA A 320 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE A 274 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLY A 211 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE A 341 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 213 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 246 through 251 removed outlier: 6.220A pdb=" N THR B 246 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N PHE B 283 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 248 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ASP B 285 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B 250 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER B 280 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE B 328 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL B 282 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA B 330 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 284 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 210 through 213 removed outlier: 5.941A pdb=" N THR C 210 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N PHE C 247 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE C 212 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER C 244 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE C 292 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE C 246 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ALA C 294 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N MET C 248 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASN C 296 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG C 313 " --> pdb=" O GLY C 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 110 through 114 removed outlier: 7.744A pdb=" N THR D 100 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ALA D 95 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS D 133 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU D 139 " --> pdb=" O HIS D 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 110 through 114 removed outlier: 7.744A pdb=" N THR D 100 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ALA D 95 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ARG E 78 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS E 68 " --> pdb=" O GLN E 63 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLN E 63 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE E 70 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU E 59 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 227 through 231 removed outlier: 7.062A pdb=" N GLY D 201 " --> pdb=" O ARG D 329 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE D 331 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU D 203 " --> pdb=" O ILE D 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 55 through 56 removed outlier: 3.838A pdb=" N ALA F 122 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL F 123 " --> pdb=" O GLU F 95 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLU F 95 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LYS F 125 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL F 93 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU F 150 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N THR F 163 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLY F 152 " --> pdb=" O LEU F 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 194 through 199 removed outlier: 6.681A pdb=" N ASN E 194 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N PHE E 231 " --> pdb=" O ASN E 194 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU E 196 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ASP E 233 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL E 198 " --> pdb=" O ASP E 233 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N CYS E 228 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE E 276 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE E 230 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ALA E 278 " --> pdb=" O ILE E 230 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N MET E 232 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 247 through 252 removed outlier: 6.061A pdb=" N THR F 247 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE F 284 " --> pdb=" O THR F 247 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU F 249 " --> pdb=" O PHE F 284 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP F 286 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU F 251 " --> pdb=" O ASP F 286 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER F 281 " --> pdb=" O LYS F 327 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE F 329 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE F 283 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ALA F 331 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE F 285 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY F 222 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE F 352 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU F 224 " --> pdb=" O ILE F 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 165 through 167 removed outlier: 4.714A pdb=" N THR G 221 " --> pdb=" O LYS G 226 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS G 226 " --> pdb=" O THR G 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 69 through 73 removed outlier: 5.238A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS G 161 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 160 through 163 Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 69 removed outlier: 6.415A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER H 133 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 34 through 36 Processing sheet with id=AB8, first strand: chain 'I' and resid 42 through 44 Processing sheet with id=AB9, first strand: chain 'I' and resid 66 through 69 removed outlier: 6.477A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 66 through 69 removed outlier: 6.477A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 158 through 161 removed outlier: 6.346A pdb=" N VAL J 33 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLY J 44 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU J 208 " --> pdb=" O LEU J 220 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 69 through 70 removed outlier: 3.904A pdb=" N CYS J 70 " --> pdb=" O VAL J 134 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL J 134 " --> pdb=" O CYS J 70 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY J 135 " --> pdb=" O ARG J 143 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG J 143 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU J 144 " --> pdb=" O TRP J 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 167 through 170 Processing sheet with id=AC5, first strand: chain 'K' and resid 67 through 71 removed outlier: 6.746A pdb=" N ILE K 67 " --> pdb=" O MET K 78 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N MET K 78 " --> pdb=" O ILE K 67 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLU K 69 " --> pdb=" O CYS K 76 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS K 76 " --> pdb=" O GLU K 69 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 158 through 161 removed outlier: 5.080A pdb=" N GLY L 216 " --> pdb=" O GLU L 220 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLU L 220 " --> pdb=" O GLY L 216 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 63 through 65 Processing sheet with id=AC8, first strand: chain 'M' and resid 162 through 165 Processing sheet with id=AC9, first strand: chain 'M' and resid 67 through 70 removed outlier: 6.189A pdb=" N VAL M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'U' and resid 744 through 746 Processing sheet with id=AD2, first strand: chain 'U' and resid 882 through 883 removed outlier: 3.920A pdb=" N ALA U 882 " --> pdb=" O VAL U 788 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N CYS U 787 " --> pdb=" O GLY U 910 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'V' and resid 449 through 452 removed outlier: 7.772A pdb=" N SER V 415 " --> pdb=" O SER V 460 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR V 414 " --> pdb=" O CYS Y 345 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ILE Y 347 " --> pdb=" O TYR V 414 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG Y 312 " --> pdb=" O THR Y 356 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LEU X 378 " --> pdb=" O ARG Y 312 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU Y 314 " --> pdb=" O LEU X 378 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'W' and resid 331 through 332 Processing sheet with id=AD5, first strand: chain 'W' and resid 405 through 407 removed outlier: 7.455A pdb=" N GLU a 326 " --> pdb=" O THR W 371 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE W 373 " --> pdb=" O GLU a 326 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Z' and resid 154 through 157 removed outlier: 10.472A pdb=" N VAL Z 120 " --> pdb=" O ARG Z 90 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL Z 92 " --> pdb=" O VAL Z 120 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL Z 122 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TRP Z 94 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE Z 124 " --> pdb=" O TRP Z 94 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N HIS Z 96 " --> pdb=" O ILE Z 124 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE Z 91 " --> pdb=" O GLY Z 41 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY Z 41 " --> pdb=" O ILE Z 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY Z 93 " --> pdb=" O LEU Z 39 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL Z 36 " --> pdb=" O ALA Z 55 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA Z 55 " --> pdb=" O VAL Z 36 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL Z 38 " --> pdb=" O SER Z 53 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER Z 53 " --> pdb=" O VAL Z 38 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU Z 40 " --> pdb=" O SER Z 51 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS Z 8 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL Z 50 " --> pdb=" O LYS Z 8 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL Z 10 " --> pdb=" O VAL Z 50 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASN Z 52 " --> pdb=" O VAL Z 10 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 58 through 60 Processing sheet with id=AD8, first strand: chain 'b' and resid 62 through 65 removed outlier: 5.094A pdb=" N THR b 63 " --> pdb=" O LEU b 51 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU b 51 " --> pdb=" O THR b 63 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N MET b 107 " --> pdb=" O ASN b 137 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ASP b 139 " --> pdb=" O MET b 107 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE b 109 " --> pdb=" O ASP b 139 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE b 141 " --> pdb=" O ILE b 109 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA b 111 " --> pdb=" O ILE b 141 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N VAL b 171 " --> pdb=" O VAL b 138 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE b 140 " --> pdb=" O VAL b 171 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'c' and resid 200 through 203 removed outlier: 4.437A pdb=" N ALA c 159 " --> pdb=" O ILE c 203 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL c 108 " --> pdb=" O GLY c 59 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY c 59 " --> pdb=" O VAL c 108 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N MET c 54 " --> pdb=" O ALA c 74 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ALA c 74 " --> pdb=" O MET c 54 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU c 56 " --> pdb=" O VAL c 72 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL c 72 " --> pdb=" O LEU c 56 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU c 58 " --> pdb=" O ILE c 70 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL c 62 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR c 66 " --> pdb=" O VAL c 62 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR c 32 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ASP c 71 " --> pdb=" O TYR c 32 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL c 31 " --> pdb=" O ASN c 206 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 281 through 283 Processing sheet with id=AE2, first strand: chain 'f' and resid 776 through 777 Processing sheet with id=AE3, first strand: chain 'f' and resid 781 through 782 Processing sheet with id=AE4, first strand: chain 'f' and resid 872 through 873 removed outlier: 6.488A pdb=" N MET f 829 " --> pdb=" O GLY f 896 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL f 898 " --> pdb=" O MET f 829 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL f 831 " --> pdb=" O VAL f 898 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU f 900 " --> pdb=" O VAL f 831 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE f 833 " --> pdb=" O LEU f 900 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LYS f 902 " --> pdb=" O PHE f 833 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'f' and resid 862 through 869 removed outlier: 5.719A pdb=" N GLY f 864 " --> pdb=" O GLN f 848 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLN f 848 " --> pdb=" O GLY f 864 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'g' and resid 98 through 104 Processing sheet with id=AE7, first strand: chain 'u' and resid 124 through 125 removed outlier: 6.785A pdb=" N ILE u 266 " --> pdb=" O TYR u 178 " (cutoff:3.500A) removed outlier: 12.538A pdb=" N VAL u 169 " --> pdb=" O PHE u 247 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N PHE u 247 " --> pdb=" O VAL u 169 " (cutoff:3.500A) removed outlier: 12.413A pdb=" N PHE u 171 " --> pdb=" O THR u 245 " (cutoff:3.500A) removed outlier: 11.935A pdb=" N THR u 245 " --> pdb=" O PHE u 171 " (cutoff:3.500A) removed outlier: 11.196A pdb=" N GLN u 173 " --> pdb=" O SER u 243 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N SER u 243 " --> pdb=" O GLN u 173 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS u 195 " --> pdb=" O PHE u 247 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'u' and resid 124 through 125 removed outlier: 6.785A pdb=" N ILE u 266 " --> pdb=" O TYR u 178 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'u' and resid 157 through 158 3828 hydrogen bonds defined for protein. 11007 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: 27.93 Time building geometry restraints manager: 16.03 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: 13264 1.31 - 1.44: 16131 1.44 - 1.57: 41530 1.57 - 1.70: 15 1.70 - 1.83: 623 Bond restraints: 71563 Sorted by residual: bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.339 0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.340 0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C5 ADP C 501 " pdb=" C6 ADP C 501 " ideal model delta sigma weight residual 1.490 1.374 0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C5 ADP B 501 " pdb=" C6 ADP B 501 " ideal model delta sigma weight residual 1.490 1.377 0.113 2.00e-02 2.50e+03 3.17e+01 ... (remaining 71558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 92832 4.07 - 8.14: 3808 8.14 - 12.22: 78 12.22 - 16.29: 6 16.29 - 20.36: 5 Bond angle restraints: 96729 Sorted by residual: angle pdb=" PA ATP F 501 " pdb=" O3A ATP F 501 " pdb=" PB ATP F 501 " ideal model delta sigma weight residual 136.83 117.24 19.59 1.00e+00 1.00e+00 3.84e+02 angle pdb=" PB ATP F 501 " pdb=" O3B ATP F 501 " pdb=" PG ATP F 501 " ideal model delta sigma weight residual 139.87 120.93 18.94 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 126.02 13.85 1.00e+00 1.00e+00 1.92e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 124.80 12.03 1.00e+00 1.00e+00 1.45e+02 angle pdb=" CA ILE A 403 " pdb=" CB ILE A 403 " pdb=" CG1 ILE A 403 " ideal model delta sigma weight residual 110.40 128.50 -18.10 1.70e+00 3.46e-01 1.13e+02 ... (remaining 96724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.76: 41438 25.76 - 51.52: 2082 51.52 - 77.29: 334 77.29 - 103.05: 73 103.05 - 128.81: 3 Dihedral angle restraints: 43930 sinusoidal: 17891 harmonic: 26039 Sorted by residual: dihedral pdb=" CA LEU b 22 " pdb=" C LEU b 22 " pdb=" N PRO b 23 " pdb=" CA PRO b 23 " ideal model delta harmonic sigma weight residual -180.00 -51.19 -128.81 0 5.00e+00 4.00e-02 6.64e+02 dihedral pdb=" CA THR B 53 " pdb=" C THR B 53 " pdb=" N PRO B 54 " pdb=" CA PRO B 54 " ideal model delta harmonic sigma weight residual 180.00 57.83 122.17 0 5.00e+00 4.00e-02 5.97e+02 dihedral pdb=" CD ARG B 303 " pdb=" NE ARG B 303 " pdb=" CZ ARG B 303 " pdb=" NH1 ARG B 303 " ideal model delta sinusoidal sigma weight residual 0.00 -62.98 62.98 1 1.00e+01 1.00e-02 5.24e+01 ... (remaining 43927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 9017 0.138 - 0.275: 1832 0.275 - 0.413: 182 0.413 - 0.551: 25 0.551 - 0.689: 7 Chirality restraints: 11063 Sorted by residual: chirality pdb=" CA LYS c 215 " pdb=" N LYS c 215 " pdb=" C LYS c 215 " pdb=" CB LYS c 215 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CA LEU B 255 " pdb=" N LEU B 255 " pdb=" C LEU B 255 " pdb=" CB LEU B 255 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CB ILE A 403 " pdb=" CA ILE A 403 " pdb=" CG1 ILE A 403 " pdb=" CG2 ILE A 403 " both_signs ideal model delta sigma weight residual False 2.64 2.01 0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 11060 not shown) Planarity restraints: 12470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR c 65 " -0.276 2.00e-02 2.50e+03 1.49e-01 4.42e+02 pdb=" CG TYR c 65 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR c 65 " 0.146 2.00e-02 2.50e+03 pdb=" CD2 TYR c 65 " 0.119 2.00e-02 2.50e+03 pdb=" CE1 TYR c 65 " 0.067 2.00e-02 2.50e+03 pdb=" CE2 TYR c 65 " 0.088 2.00e-02 2.50e+03 pdb=" CZ TYR c 65 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR c 65 " -0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP U 770 " -0.215 2.00e-02 2.50e+03 1.16e-01 3.37e+02 pdb=" CG TRP U 770 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP U 770 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP U 770 " 0.120 2.00e-02 2.50e+03 pdb=" NE1 TRP U 770 " 0.084 2.00e-02 2.50e+03 pdb=" CE2 TRP U 770 " 0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP U 770 " 0.164 2.00e-02 2.50e+03 pdb=" CZ2 TRP U 770 " -0.132 2.00e-02 2.50e+03 pdb=" CZ3 TRP U 770 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP U 770 " -0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR U 590 " -0.191 2.00e-02 2.50e+03 1.02e-01 2.09e+02 pdb=" CG TYR U 590 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR U 590 " 0.084 2.00e-02 2.50e+03 pdb=" CD2 TYR U 590 " 0.091 2.00e-02 2.50e+03 pdb=" CE1 TYR U 590 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TYR U 590 " 0.043 2.00e-02 2.50e+03 pdb=" CZ TYR U 590 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR U 590 " -0.148 2.00e-02 2.50e+03 ... (remaining 12467 not shown) Histogram of nonbonded interaction distances: 0.64 - 1.49: 15 1.49 - 2.34: 65 2.34 - 3.20: 66715 3.20 - 4.05: 185507 4.05 - 4.90: 326975 Warning: very small nonbonded interaction distances. Nonbonded interactions: 579277 Sorted by model distance: nonbonded pdb=" CA TYR D 392 " pdb=" CZ ARG E 161 " model vdw 0.641 3.700 nonbonded pdb=" CB TYR D 392 " pdb=" NE ARG E 161 " model vdw 0.786 3.520 nonbonded pdb=" C TYR D 392 " pdb=" NH1 ARG E 161 " model vdw 0.804 3.350 nonbonded pdb=" CA TYR D 392 " pdb=" NH2 ARG E 161 " model vdw 0.847 3.550 nonbonded pdb=" CB TYR D 392 " pdb=" CZ ARG E 161 " model vdw 0.962 3.670 ... (remaining 579272 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 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: 0.050 Extract box with map and model: 2.280 Check model and map are aligned: 0.420 Set scattering table: 0.490 Process input model: 129.930 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.230 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:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 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 0.151 71563 Z= 0.811 Angle : 1.925 20.360 96729 Z= 1.283 Chirality : 0.110 0.689 11063 Planarity : 0.018 0.446 12470 Dihedral : 15.796 128.811 27071 Min Nonbonded Distance : 0.641 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 2.09 % Allowed : 8.23 % Favored : 89.68 % Rotamer: Outliers : 4.80 % Allowed : 8.74 % Favored : 86.47 % Cbeta Deviations : 0.90 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: -2.62 (0.08), residues: 8837 helix: -1.56 (0.06), residues: 4677 sheet: -0.60 (0.17), residues: 840 loop : -2.11 (0.10), residues: 3320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.215 0.027 TRP U 770 HIS 0.022 0.004 HIS A 150 PHE 0.120 0.014 PHE c 61 TYR 0.276 0.023 TYR c 65 ARG 0.015 0.001 ARG c 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2612 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 365 poor density : 2247 time to evaluate : 7.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8364 (tppt) REVERT: A 249 TYR cc_start: 0.6086 (m-80) cc_final: 0.5232 (m-10) REVERT: A 337 LEU cc_start: 0.7670 (mt) cc_final: 0.7443 (mt) REVERT: A 422 LYS cc_start: 0.5742 (OUTLIER) cc_final: 0.5199 (ttpp) REVERT: B 118 ASP cc_start: 0.6577 (p0) cc_final: 0.6353 (p0) REVERT: B 192 ASN cc_start: 0.8105 (m110) cc_final: 0.7639 (m-40) REVERT: C 66 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8928 (mt) REVERT: E 149 ILE cc_start: 0.9060 (mm) cc_final: 0.8795 (mp) REVERT: E 322 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7346 (pttm) REVERT: F 53 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.6280 (tptt) REVERT: F 71 ASP cc_start: 0.8100 (m-30) cc_final: 0.7559 (m-30) REVERT: F 144 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8098 (mmmt) REVERT: F 209 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7859 (mtmm) REVERT: F 212 PHE cc_start: 0.7454 (m-80) cc_final: 0.6772 (m-80) REVERT: F 223 VAL cc_start: 0.8846 (t) cc_final: 0.8601 (p) REVERT: F 343 LEU cc_start: 0.7932 (mt) cc_final: 0.7420 (mt) REVERT: G 80 MET cc_start: 0.6224 (mmm) cc_final: 0.5818 (mmm) REVERT: H 79 MET cc_start: 0.6625 (pmm) cc_final: 0.6173 (tpt) REVERT: I 56 LEU cc_start: 0.4765 (OUTLIER) cc_final: 0.4402 (tp) REVERT: J 69 VAL cc_start: 0.3213 (OUTLIER) cc_final: 0.2941 (t) REVERT: L 138 ASP cc_start: 0.5919 (OUTLIER) cc_final: 0.5270 (m-30) REVERT: M 184 MET cc_start: 0.3706 (mtp) cc_final: 0.3105 (mtp) REVERT: M 185 THR cc_start: 0.4578 (t) cc_final: 0.3997 (t) REVERT: U 44 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8440 (tttt) REVERT: U 69 TYR cc_start: 0.9172 (t80) cc_final: 0.8263 (t80) REVERT: U 229 VAL cc_start: 0.9378 (OUTLIER) cc_final: 0.9040 (p) REVERT: U 242 LEU cc_start: 0.8640 (mp) cc_final: 0.8144 (mt) REVERT: U 351 MET cc_start: 0.6853 (tmm) cc_final: 0.6611 (tmm) REVERT: U 371 ILE cc_start: 0.9299 (mt) cc_final: 0.9096 (mp) REVERT: U 556 MET cc_start: 0.7806 (mmt) cc_final: 0.7605 (tpt) REVERT: U 694 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7952 (tt) REVERT: U 751 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7221 (ptt-90) REVERT: U 830 THR cc_start: 0.5824 (m) cc_final: 0.2962 (m) REVERT: U 892 LEU cc_start: 0.7911 (pp) cc_final: 0.7629 (tp) REVERT: U 902 PRO cc_start: 0.8774 (Cg_endo) cc_final: 0.8181 (Cg_exo) REVERT: V 38 LYS cc_start: 0.8936 (mtmt) cc_final: 0.8681 (ptpp) REVERT: V 176 MET cc_start: 0.7892 (mmp) cc_final: 0.7196 (ptp) REVERT: V 245 ASP cc_start: 0.6984 (m-30) cc_final: 0.6740 (m-30) REVERT: V 400 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.6780 (m170) REVERT: W 73 MET cc_start: 0.8021 (mmm) cc_final: 0.7806 (tpt) REVERT: W 276 LEU cc_start: 0.7688 (mt) cc_final: 0.6652 (tp) REVERT: W 407 ASP cc_start: 0.6048 (t0) cc_final: 0.5831 (t0) REVERT: Y 59 LYS cc_start: 0.8650 (pttt) cc_final: 0.8269 (mmtt) REVERT: Y 381 GLN cc_start: 0.7898 (tt0) cc_final: 0.7603 (tt0) REVERT: Z 52 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8444 (m-40) REVERT: Z 68 TRP cc_start: 0.8421 (p-90) cc_final: 0.8111 (p-90) REVERT: a 21 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8724 (m) REVERT: a 26 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: a 138 VAL cc_start: 0.8794 (t) cc_final: 0.8575 (t) REVERT: a 142 LEU cc_start: 0.8831 (tp) cc_final: 0.8533 (mt) REVERT: a 272 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7832 (tp) REVERT: a 281 THR cc_start: 0.7996 (p) cc_final: 0.6727 (t) REVERT: a 282 PHE cc_start: 0.7744 (t80) cc_final: 0.7412 (t80) REVERT: a 307 VAL cc_start: 0.6156 (m) cc_final: 0.5769 (m) REVERT: b 1 MET cc_start: 0.3632 (mtp) cc_final: 0.1989 (tpt) REVERT: b 84 ILE cc_start: 0.8937 (mm) cc_final: 0.8720 (mm) REVERT: b 97 LEU cc_start: 0.8186 (tp) cc_final: 0.7691 (tp) REVERT: b 135 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7087 (tmtt) REVERT: c 72 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7453 (t) REVERT: c 107 MET cc_start: 0.7146 (pp-130) cc_final: 0.6843 (ppp) REVERT: c 187 PRO cc_start: 0.8309 (Cg_endo) cc_final: 0.8103 (Cg_exo) REVERT: d 108 ASN cc_start: 0.8753 (t0) cc_final: 0.8330 (t0) REVERT: d 122 VAL cc_start: 0.8066 (m) cc_final: 0.7496 (m) REVERT: d 148 LEU cc_start: 0.9229 (mt) cc_final: 0.9018 (tp) REVERT: d 200 LEU cc_start: 0.9048 (mp) cc_final: 0.8832 (mt) REVERT: e 59 GLU cc_start: 0.7325 (tp30) cc_final: 0.6512 (tp30) REVERT: f 65 GLU cc_start: 0.5176 (OUTLIER) cc_final: 0.4824 (pp20) REVERT: f 177 GLU cc_start: 0.3692 (OUTLIER) cc_final: 0.2476 (pm20) REVERT: f 309 GLU cc_start: 0.7498 (tp30) cc_final: 0.7201 (pm20) REVERT: f 347 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.8521 (p0) REVERT: f 440 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8132 (pt) REVERT: f 463 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7723 (mt) REVERT: g 119 THR cc_start: 0.6515 (m) cc_final: 0.6122 (p) REVERT: u 199 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8264 (m-40) REVERT: u 240 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8143 (p0) outliers start: 365 outliers final: 84 residues processed: 2502 average time/residue: 0.7260 time to fit residues: 2987.1779 Evaluate side-chains 1255 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1144 time to evaluate : 6.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain F residue 351 LYS Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain M residue 99 ARG Chi-restraints excluded: chain U residue 98 GLU Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 229 VAL Chi-restraints excluded: chain U residue 231 ASP Chi-restraints excluded: chain U residue 366 HIS Chi-restraints excluded: chain U residue 694 ILE Chi-restraints excluded: chain U residue 751 ARG Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain V residue 65 ARG Chi-restraints excluded: chain V residue 194 LYS Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 230 PHE Chi-restraints excluded: chain V residue 270 LEU Chi-restraints excluded: chain V residue 361 PHE Chi-restraints excluded: chain V residue 400 HIS Chi-restraints excluded: chain V residue 491 VAL Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 263 TRP Chi-restraints excluded: chain W residue 387 ASP Chi-restraints excluded: chain X residue 388 PHE Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Z residue 52 ASN Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 189 GLN Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 54 ASP Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain a residue 137 ASP Chi-restraints excluded: chain a residue 272 ILE Chi-restraints excluded: chain a residue 334 THR Chi-restraints excluded: chain a residue 350 LYS Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 135 LYS Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain c residue 205 ILE Chi-restraints excluded: chain c residue 256 ASN Chi-restraints excluded: chain d residue 198 PHE Chi-restraints excluded: chain d residue 211 GLU Chi-restraints excluded: chain d residue 260 ILE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 65 GLU Chi-restraints excluded: chain f residue 177 GLU Chi-restraints excluded: chain f residue 300 ARG Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 463 LEU Chi-restraints excluded: chain f residue 552 ASP Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 787 LEU Chi-restraints excluded: chain f residue 850 VAL Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 167 ILE Chi-restraints excluded: chain u residue 182 PHE Chi-restraints excluded: chain u residue 199 ASN Chi-restraints excluded: chain u residue 224 ASP Chi-restraints excluded: chain u residue 225 ILE Chi-restraints excluded: chain u residue 240 ASN Chi-restraints excluded: chain u residue 289 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 743 optimal weight: 2.9990 chunk 666 optimal weight: 0.9980 chunk 370 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 449 optimal weight: 4.9990 chunk 356 optimal weight: 9.9990 chunk 689 optimal weight: 0.0470 chunk 266 optimal weight: 3.9990 chunk 419 optimal weight: 5.9990 chunk 513 optimal weight: 7.9990 chunk 799 optimal weight: 0.7980 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 247 GLN A 379 ASN B 154 HIS B 181 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS C 171 HIS ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS E 19 HIS E 124 HIS ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 207 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN I 155 ASN I 198 ASN ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN K 182 GLN M 97 ASN M 105 ASN ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 145 HIS U 362 ASN U 453 HIS V 326 GLN V 453 HIS V 477 HIS V 488 ASN W 170 GLN W 246 HIS W 453 HIS X 44 GLN X 262 ASN ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 154 ASN Y 273 GLN Y 388 ASN Z 7 GLN ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 157 HIS Z 189 GLN Z 229 GLN a 193 GLN ** a 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 92 GLN c 101 GLN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 131 GLN c 197 ASN c 219 ASN c 237 HIS d 234 GLN e 63 HIS ** f 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 540 GLN ** f 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 876 HIS ** g 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 199 ASN u 240 ASN ** u 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.078404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.061475 restraints weight = 374600.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.063293 restraints weight = 206805.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.064478 restraints weight = 134382.285| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 71563 Z= 0.284 Angle : 0.922 14.295 96729 Z= 0.475 Chirality : 0.050 0.352 11063 Planarity : 0.006 0.118 12470 Dihedral : 9.229 122.834 10026 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.03 % Favored : 93.37 % Rotamer: Outliers : 4.90 % Allowed : 16.12 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.09), residues: 8837 helix: -0.24 (0.07), residues: 4788 sheet: -0.42 (0.16), residues: 915 loop : -1.38 (0.12), residues: 3134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP d 154 HIS 0.013 0.002 HIS V 62 PHE 0.042 0.003 PHE W 279 TYR 0.033 0.002 TYR M 238 ARG 0.031 0.001 ARG E 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1664 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 373 poor density : 1291 time to evaluate : 6.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ILE cc_start: 0.8839 (tt) cc_final: 0.8587 (tp) REVERT: A 100 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8182 (ttmm) REVERT: A 187 LEU cc_start: 0.9770 (OUTLIER) cc_final: 0.9547 (pp) REVERT: A 259 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8428 (mp0) REVERT: A 299 MET cc_start: 0.8996 (tmm) cc_final: 0.8493 (ppp) REVERT: A 300 LEU cc_start: 0.9534 (mt) cc_final: 0.8931 (mt) REVERT: A 307 ASP cc_start: 0.7915 (t0) cc_final: 0.7648 (t0) REVERT: A 337 LEU cc_start: 0.9419 (mt) cc_final: 0.9142 (mt) REVERT: B 55 HIS cc_start: 0.7892 (m90) cc_final: 0.7624 (m90) REVERT: B 69 LYS cc_start: 0.9340 (tttp) cc_final: 0.9062 (mtpt) REVERT: B 107 MET cc_start: 0.8466 (mpp) cc_final: 0.8163 (mpp) REVERT: B 114 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8493 (mt-10) REVERT: B 225 TYR cc_start: 0.8409 (p90) cc_final: 0.7941 (p90) REVERT: B 338 ASP cc_start: 0.6647 (m-30) cc_final: 0.6121 (t0) REVERT: B 381 ASP cc_start: 0.8668 (m-30) cc_final: 0.8383 (p0) REVERT: B 385 MET cc_start: 0.7864 (ppp) cc_final: 0.7553 (ppp) REVERT: B 401 GLU cc_start: 0.8805 (tp30) cc_final: 0.8478 (tt0) REVERT: B 404 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9213 (mm) REVERT: C 62 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8323 (tm-30) REVERT: C 66 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8575 (mp) REVERT: C 81 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8359 (p0) REVERT: C 129 ASN cc_start: 0.9208 (p0) cc_final: 0.9005 (p0) REVERT: C 368 MET cc_start: 0.9170 (mmm) cc_final: 0.8957 (tpp) REVERT: C 385 MET cc_start: 0.8736 (ptt) cc_final: 0.8398 (ptt) REVERT: D 71 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8434 (tp30) REVERT: D 97 ASP cc_start: 0.8935 (t0) cc_final: 0.8606 (t0) REVERT: D 141 ASP cc_start: 0.8349 (t0) cc_final: 0.8005 (t0) REVERT: D 192 LYS cc_start: 0.9275 (ttpt) cc_final: 0.8955 (ttmt) REVERT: D 215 LEU cc_start: 0.9193 (tp) cc_final: 0.8977 (tp) REVERT: D 222 HIS cc_start: 0.8244 (OUTLIER) cc_final: 0.7958 (m90) REVERT: E 86 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7159 (pm20) REVERT: E 215 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7852 (tt) REVERT: E 236 ASP cc_start: 0.9071 (p0) cc_final: 0.8645 (p0) REVERT: E 277 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7926 (mmt) REVERT: F 53 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6621 (pttt) REVERT: F 71 ASP cc_start: 0.8708 (m-30) cc_final: 0.8414 (m-30) REVERT: F 206 MET cc_start: 0.8913 (mmm) cc_final: 0.8194 (mmt) REVERT: G 80 MET cc_start: 0.6889 (mmm) cc_final: 0.6105 (mmm) REVERT: G 228 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8158 (ptp-170) REVERT: H 79 MET cc_start: 0.5852 (pmm) cc_final: 0.5485 (tpt) REVERT: H 89 ARG cc_start: 0.8692 (tpp80) cc_final: 0.8427 (mmp-170) REVERT: H 177 ARG cc_start: 0.8931 (tpp-160) cc_final: 0.8592 (tpp80) REVERT: I 25 MET cc_start: 0.9085 (mtt) cc_final: 0.8740 (mpp) REVERT: I 198 ASN cc_start: 0.7415 (t0) cc_final: 0.6768 (m-40) REVERT: J 15 HIS cc_start: 0.8205 (m90) cc_final: 0.7953 (m90) REVERT: J 172 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7845 (mp) REVERT: K 8 TYR cc_start: 0.2137 (m-80) cc_final: 0.1427 (m-80) REVERT: K 229 PHE cc_start: 0.7182 (m-80) cc_final: 0.6916 (m-10) REVERT: L 46 LEU cc_start: 0.4098 (OUTLIER) cc_final: 0.3836 (pp) REVERT: M 58 TYR cc_start: 0.6552 (t80) cc_final: 0.5992 (t80) REVERT: M 66 LEU cc_start: 0.6376 (OUTLIER) cc_final: 0.6019 (mp) REVERT: M 135 PHE cc_start: 0.8835 (p90) cc_final: 0.8634 (p90) REVERT: M 150 MET cc_start: 0.7892 (tmm) cc_final: 0.7592 (tmm) REVERT: M 180 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7910 (tm-30) REVERT: U 35 TRP cc_start: 0.9043 (p-90) cc_final: 0.8562 (p-90) REVERT: U 44 LYS cc_start: 0.9016 (mtmt) cc_final: 0.8594 (tttt) REVERT: U 95 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7806 (tm-30) REVERT: U 244 MET cc_start: 0.8724 (mmm) cc_final: 0.8434 (mmm) REVERT: U 251 ASP cc_start: 0.8516 (m-30) cc_final: 0.8273 (m-30) REVERT: U 466 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8691 (pttp) REVERT: U 556 MET cc_start: 0.7974 (mmt) cc_final: 0.7585 (tpt) REVERT: U 609 ASP cc_start: 0.7920 (t0) cc_final: 0.7686 (t0) REVERT: U 738 ASP cc_start: 0.8904 (m-30) cc_final: 0.8667 (m-30) REVERT: U 778 PHE cc_start: 0.9120 (m-80) cc_final: 0.8889 (m-10) REVERT: V 38 LYS cc_start: 0.9094 (mtmt) cc_final: 0.8791 (ptpp) REVERT: V 400 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.8116 (m-70) REVERT: V 494 MET cc_start: 0.8882 (mmm) cc_final: 0.8562 (tpp) REVERT: W 73 MET cc_start: 0.8904 (mmm) cc_final: 0.8319 (tpt) REVERT: W 174 TYR cc_start: 0.6777 (m-80) cc_final: 0.6395 (m-80) REVERT: W 230 MET cc_start: 0.8673 (tpt) cc_final: 0.8465 (mmt) REVERT: W 425 LEU cc_start: 0.9620 (mt) cc_final: 0.9365 (mp) REVERT: X 153 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8395 (tt) REVERT: X 162 ASP cc_start: 0.7990 (t0) cc_final: 0.7771 (t0) REVERT: X 301 ASP cc_start: 0.8523 (t0) cc_final: 0.8264 (t0) REVERT: X 315 ASP cc_start: 0.8191 (m-30) cc_final: 0.7971 (p0) REVERT: Y 59 LYS cc_start: 0.8976 (pttt) cc_final: 0.8721 (mmtt) REVERT: Y 196 GLN cc_start: 0.8680 (mt0) cc_final: 0.8204 (mp10) REVERT: Y 282 MET cc_start: 0.8726 (tpp) cc_final: 0.8412 (tpp) REVERT: Y 288 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8486 (t80) REVERT: Y 314 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9236 (pp) REVERT: Z 68 TRP cc_start: 0.8175 (p-90) cc_final: 0.7877 (p-90) REVERT: Z 88 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7662 (mtt-85) REVERT: a 26 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8359 (tm-30) REVERT: a 141 MET cc_start: 0.8546 (ptm) cc_final: 0.8120 (ppp) REVERT: a 142 LEU cc_start: 0.9074 (tp) cc_final: 0.8725 (mt) REVERT: a 175 ASP cc_start: 0.8827 (m-30) cc_final: 0.8198 (t70) REVERT: a 218 MET cc_start: 0.7733 (mtp) cc_final: 0.7322 (mtm) REVERT: a 272 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.7863 (tp) REVERT: a 276 CYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8133 (p) REVERT: a 278 MET cc_start: 0.9171 (mmm) cc_final: 0.8117 (mpp) REVERT: a 281 THR cc_start: 0.8470 (p) cc_final: 0.7637 (t) REVERT: a 282 PHE cc_start: 0.8482 (t80) cc_final: 0.8148 (t80) REVERT: b 1 MET cc_start: 0.3736 (mtp) cc_final: 0.1955 (tpt) REVERT: b 7 MET cc_start: 0.8725 (mmm) cc_final: 0.8397 (mmm) REVERT: b 16 MET cc_start: 0.8282 (tpt) cc_final: 0.7734 (tpp) REVERT: c 107 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7394 (ppp) REVERT: c 303 MET cc_start: 0.8768 (mmm) cc_final: 0.8527 (mmm) REVERT: d 94 MET cc_start: 0.8149 (ptp) cc_final: 0.7889 (ptm) REVERT: d 108 ASN cc_start: 0.8701 (t0) cc_final: 0.8485 (t0) REVERT: d 160 ASP cc_start: 0.7702 (t0) cc_final: 0.7437 (t0) REVERT: d 194 LEU cc_start: 0.8744 (mt) cc_final: 0.8372 (mt) REVERT: d 299 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8318 (mmm) REVERT: e 59 GLU cc_start: 0.8234 (tp30) cc_final: 0.7597 (tp30) REVERT: f 177 GLU cc_start: 0.3916 (OUTLIER) cc_final: 0.3387 (pm20) REVERT: f 268 LEU cc_start: 0.9415 (mp) cc_final: 0.9035 (tt) REVERT: f 275 MET cc_start: 0.8265 (mtm) cc_final: 0.7752 (mtt) REVERT: f 294 MET cc_start: 0.7822 (ptp) cc_final: 0.7361 (ptp) REVERT: f 297 MET cc_start: 0.9224 (mtt) cc_final: 0.8969 (mtt) REVERT: f 309 GLU cc_start: 0.8408 (tp30) cc_final: 0.7719 (pm20) REVERT: f 340 MET cc_start: 0.6025 (mmm) cc_final: 0.5725 (mmm) REVERT: f 347 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8732 (p0) REVERT: f 416 MET cc_start: 0.8977 (mtm) cc_final: 0.8419 (mtm) REVERT: f 678 LEU cc_start: 0.9239 (mp) cc_final: 0.8944 (tp) REVERT: f 731 MET cc_start: 0.9316 (tpt) cc_final: 0.9054 (tpp) REVERT: f 744 MET cc_start: 0.9265 (mtt) cc_final: 0.9050 (mpp) REVERT: f 788 MET cc_start: 0.7861 (ptm) cc_final: 0.6985 (ttp) REVERT: u 178 TYR cc_start: 0.8692 (t80) cc_final: 0.8204 (t80) REVERT: u 180 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8522 (ppp) REVERT: u 266 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8469 (tp) outliers start: 373 outliers final: 173 residues processed: 1553 average time/residue: 0.6740 time to fit residues: 1773.6111 Evaluate side-chains 1166 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 965 time to evaluate : 6.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 222 HIS Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 351 LYS Chi-restraints excluded: chain F residue 437 TYR Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 228 ARG Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 98 GLU Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 252 LEU Chi-restraints excluded: chain U residue 262 SER Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 366 HIS Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 411 ILE Chi-restraints excluded: chain U residue 466 LYS Chi-restraints excluded: chain U residue 486 MET Chi-restraints excluded: chain U residue 593 SER Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 675 MET Chi-restraints excluded: chain U residue 685 GLN Chi-restraints excluded: chain U residue 706 VAL Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 135 LEU Chi-restraints excluded: chain V residue 144 ASP Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 194 LYS Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 230 PHE Chi-restraints excluded: chain V residue 249 THR Chi-restraints excluded: chain V residue 303 SER Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 400 HIS Chi-restraints excluded: chain V residue 453 HIS Chi-restraints excluded: chain V residue 464 ILE Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 427 ASP Chi-restraints excluded: chain W residue 438 LEU Chi-restraints excluded: chain X residue 153 LEU Chi-restraints excluded: chain X residue 177 TYR Chi-restraints excluded: chain X residue 388 PHE Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 204 THR Chi-restraints excluded: chain Y residue 288 PHE Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 330 ILE Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 108 ILE Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 135 THR Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 182 THR Chi-restraints excluded: chain Z residue 195 VAL Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 278 ASN Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 272 ILE Chi-restraints excluded: chain a residue 275 LEU Chi-restraints excluded: chain a residue 276 CYS Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 107 MET Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 122 LEU Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 131 GLN Chi-restraints excluded: chain c residue 179 SER Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 205 ILE Chi-restraints excluded: chain c residue 218 LEU Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain e residue 65 TYR Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 113 MET Chi-restraints excluded: chain f residue 177 GLU Chi-restraints excluded: chain f residue 256 PHE Chi-restraints excluded: chain f residue 266 LEU Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain f residue 552 ASP Chi-restraints excluded: chain f residue 793 VAL Chi-restraints excluded: chain f residue 832 THR Chi-restraints excluded: chain f residue 850 VAL Chi-restraints excluded: chain f residue 905 ASN Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 130 ILE Chi-restraints excluded: chain u residue 167 ILE Chi-restraints excluded: chain u residue 180 MET Chi-restraints excluded: chain u residue 182 PHE Chi-restraints excluded: chain u residue 241 VAL Chi-restraints excluded: chain u residue 244 VAL Chi-restraints excluded: chain u residue 266 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 210 optimal weight: 3.9990 chunk 581 optimal weight: 7.9990 chunk 805 optimal weight: 5.9990 chunk 339 optimal weight: 20.0000 chunk 741 optimal weight: 20.0000 chunk 317 optimal weight: 50.0000 chunk 665 optimal weight: 0.9990 chunk 542 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 615 optimal weight: 8.9990 chunk 508 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN B 120 HIS B 154 HIS C 278 ASN D 133 HIS E 32 GLN E 160 GLN E 194 ASN ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN H 63 HIS U 89 ASN U 190 ASN ** U 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 500 ASN U 611 ASN V 453 HIS X 405 GLN Y 306 GLN Y 344 HIS Y 388 ASN Z 7 GLN Z 174 HIS Z 235 ASN ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 214 GLN ** d 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 HIS ** f 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 135 GLN ** g 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 289 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.075347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.058203 restraints weight = 381061.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.059939 restraints weight = 208811.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.061067 restraints weight = 135774.826| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 71563 Z= 0.284 Angle : 0.817 13.435 96729 Z= 0.419 Chirality : 0.047 0.322 11063 Planarity : 0.005 0.076 12470 Dihedral : 8.211 151.792 9897 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.53 % Favored : 93.05 % Rotamer: Outliers : 4.49 % Allowed : 18.19 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.04 % 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: -0.65 (0.09), residues: 8837 helix: 0.17 (0.07), residues: 4799 sheet: -0.53 (0.16), residues: 928 loop : -1.19 (0.12), residues: 3110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP a 255 HIS 0.016 0.002 HIS e 63 PHE 0.033 0.002 PHE W 279 TYR 0.030 0.002 TYR U 246 ARG 0.010 0.001 ARG V 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1368 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 342 poor density : 1026 time to evaluate : 6.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8579 (t0) cc_final: 0.8331 (t0) REVERT: A 256 MET cc_start: 0.9220 (mtp) cc_final: 0.8925 (mtp) REVERT: A 259 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8508 (mp0) REVERT: A 299 MET cc_start: 0.8980 (tmm) cc_final: 0.8694 (ppp) REVERT: A 300 LEU cc_start: 0.9524 (mt) cc_final: 0.8894 (mt) REVERT: A 307 ASP cc_start: 0.8036 (t0) cc_final: 0.7703 (t0) REVERT: B 69 LYS cc_start: 0.9346 (tttp) cc_final: 0.9112 (mmmt) REVERT: B 75 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8633 (mm-30) REVERT: B 107 MET cc_start: 0.8634 (mpp) cc_final: 0.8420 (mpp) REVERT: B 114 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8360 (mt-10) REVERT: B 118 ASP cc_start: 0.8558 (p0) cc_final: 0.8290 (p0) REVERT: B 177 GLU cc_start: 0.8498 (tp30) cc_final: 0.7891 (tt0) REVERT: B 191 ASP cc_start: 0.8369 (p0) cc_final: 0.8144 (p0) REVERT: B 225 TYR cc_start: 0.8379 (p90) cc_final: 0.8140 (p90) REVERT: B 329 MET cc_start: 0.9060 (mtm) cc_final: 0.8781 (mtm) REVERT: B 404 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9269 (mm) REVERT: B 405 MET cc_start: 0.8780 (mtp) cc_final: 0.8318 (mtp) REVERT: B 412 MET cc_start: 0.8614 (tpp) cc_final: 0.8399 (tpp) REVERT: C 62 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8686 (tm-30) REVERT: C 80 MET cc_start: 0.9053 (mmm) cc_final: 0.8841 (mmm) REVERT: C 273 MET cc_start: 0.8116 (mmm) cc_final: 0.7872 (mmm) REVERT: C 385 MET cc_start: 0.8785 (ptt) cc_final: 0.8563 (ptt) REVERT: C 399 MET cc_start: 0.7728 (mmp) cc_final: 0.7191 (mmp) REVERT: C 403 LYS cc_start: 0.5032 (OUTLIER) cc_final: 0.4804 (pttt) REVERT: D 97 ASP cc_start: 0.8999 (t0) cc_final: 0.8567 (t0) REVERT: D 141 ASP cc_start: 0.8395 (t0) cc_final: 0.8143 (t0) REVERT: D 192 LYS cc_start: 0.9259 (ttpt) cc_final: 0.8936 (ttmt) REVERT: D 214 MET cc_start: 0.8964 (tpt) cc_final: 0.8314 (mmm) REVERT: D 313 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6975 (ptp90) REVERT: D 359 ASP cc_start: 0.7803 (t0) cc_final: 0.7516 (p0) REVERT: E 86 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: E 352 MET cc_start: 0.9186 (mmt) cc_final: 0.8875 (mmt) REVERT: F 53 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6907 (pttt) REVERT: F 71 ASP cc_start: 0.8699 (m-30) cc_final: 0.8444 (m-30) REVERT: F 225 MET cc_start: 0.7879 (mtm) cc_final: 0.7134 (ptp) REVERT: F 315 ASN cc_start: 0.9092 (m-40) cc_final: 0.8610 (m-40) REVERT: F 351 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8865 (mtmm) REVERT: F 421 MET cc_start: 0.8715 (mmm) cc_final: 0.8428 (mmm) REVERT: F 437 TYR cc_start: 0.7354 (m-10) cc_final: 0.6775 (m-10) REVERT: G 138 MET cc_start: 0.8721 (tmm) cc_final: 0.8428 (tmm) REVERT: G 160 TYR cc_start: 0.7927 (p90) cc_final: 0.7007 (p90) REVERT: H 62 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7771 (m) REVERT: H 70 LYS cc_start: 0.9053 (mtmt) cc_final: 0.8603 (tptt) REVERT: H 134 LEU cc_start: 0.9544 (mt) cc_final: 0.9121 (tp) REVERT: I 198 ASN cc_start: 0.7367 (t0) cc_final: 0.6689 (m-40) REVERT: J 15 HIS cc_start: 0.8321 (m90) cc_final: 0.8030 (m90) REVERT: K 8 TYR cc_start: 0.1936 (m-80) cc_final: 0.1620 (m-10) REVERT: L 46 LEU cc_start: 0.4309 (OUTLIER) cc_final: 0.4102 (pp) REVERT: M 66 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.6084 (mp) REVERT: M 105 ASN cc_start: 0.8246 (m-40) cc_final: 0.7860 (t0) REVERT: M 150 MET cc_start: 0.8086 (tmm) cc_final: 0.7823 (tmm) REVERT: U 35 TRP cc_start: 0.8886 (p-90) cc_final: 0.8657 (p-90) REVERT: U 188 MET cc_start: 0.6323 (tpt) cc_final: 0.5539 (ppp) REVERT: U 244 MET cc_start: 0.8655 (mmm) cc_final: 0.8283 (mmm) REVERT: U 351 MET cc_start: 0.6297 (ptt) cc_final: 0.6030 (ptt) REVERT: U 609 ASP cc_start: 0.7977 (t0) cc_final: 0.7765 (t0) REVERT: U 738 ASP cc_start: 0.8901 (m-30) cc_final: 0.8671 (m-30) REVERT: U 778 PHE cc_start: 0.9232 (m-80) cc_final: 0.8876 (m-10) REVERT: V 38 LYS cc_start: 0.9075 (mtmt) cc_final: 0.8764 (mtmm) REVERT: V 78 HIS cc_start: 0.4695 (OUTLIER) cc_final: 0.4382 (p-80) REVERT: V 139 MET cc_start: 0.8974 (ptm) cc_final: 0.8248 (ppp) REVERT: V 400 HIS cc_start: 0.8655 (OUTLIER) cc_final: 0.8244 (m-70) REVERT: V 494 MET cc_start: 0.8840 (mmm) cc_final: 0.8575 (tpp) REVERT: W 73 MET cc_start: 0.8892 (mmm) cc_final: 0.8255 (tpt) REVERT: X 153 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8334 (tt) REVERT: X 162 ASP cc_start: 0.7917 (t0) cc_final: 0.7615 (t0) REVERT: X 301 ASP cc_start: 0.8606 (t0) cc_final: 0.8317 (t0) REVERT: X 373 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8426 (mtpt) REVERT: X 405 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8592 (tm-30) REVERT: Y 59 LYS cc_start: 0.8997 (pttt) cc_final: 0.8751 (mmtt) REVERT: Y 196 GLN cc_start: 0.8683 (mt0) cc_final: 0.8326 (mp10) REVERT: Y 235 ASP cc_start: 0.9033 (m-30) cc_final: 0.8719 (m-30) REVERT: Y 282 MET cc_start: 0.8764 (tpp) cc_final: 0.8322 (tpp) REVERT: Y 288 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8472 (t80) REVERT: Z 44 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8494 (mm-40) REVERT: Z 68 TRP cc_start: 0.8330 (p-90) cc_final: 0.8124 (p-90) REVERT: a 26 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8338 (tm-30) REVERT: a 87 MET cc_start: 0.7982 (ppp) cc_final: 0.7747 (ppp) REVERT: a 109 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6106 (tp30) REVERT: a 141 MET cc_start: 0.8557 (ptm) cc_final: 0.7878 (ppp) REVERT: a 142 LEU cc_start: 0.9082 (tp) cc_final: 0.8618 (mt) REVERT: a 175 ASP cc_start: 0.8996 (m-30) cc_final: 0.8490 (t70) REVERT: a 218 MET cc_start: 0.7876 (mtp) cc_final: 0.7434 (mtm) REVERT: a 278 MET cc_start: 0.9237 (mmm) cc_final: 0.8912 (mmm) REVERT: a 281 THR cc_start: 0.8562 (p) cc_final: 0.8083 (t) REVERT: a 335 TRP cc_start: 0.7591 (t60) cc_final: 0.7149 (t60) REVERT: a 365 MET cc_start: 0.8522 (ptt) cc_final: 0.8321 (ptt) REVERT: b 1 MET cc_start: 0.3799 (mtp) cc_final: 0.1724 (tpt) REVERT: b 22 LEU cc_start: 0.8475 (mp) cc_final: 0.8128 (pt) REVERT: b 70 ARG cc_start: 0.9302 (tpp80) cc_final: 0.8820 (mmm160) REVERT: b 183 LEU cc_start: 0.6545 (tp) cc_final: 0.6273 (mt) REVERT: c 148 ILE cc_start: 0.8874 (pp) cc_final: 0.8629 (pt) REVERT: c 173 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6555 (pm20) REVERT: d 108 ASN cc_start: 0.8633 (t0) cc_final: 0.8395 (t0) REVERT: d 160 ASP cc_start: 0.8021 (t0) cc_final: 0.7669 (t0) REVERT: d 168 MET cc_start: 0.9357 (tpp) cc_final: 0.9018 (tpp) REVERT: d 194 LEU cc_start: 0.9020 (mt) cc_final: 0.8708 (mt) REVERT: d 242 ASN cc_start: 0.8330 (t0) cc_final: 0.8044 (m-40) REVERT: d 299 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8473 (mmm) REVERT: d 309 VAL cc_start: 0.8067 (m) cc_final: 0.7829 (p) REVERT: e 59 GLU cc_start: 0.8311 (tp30) cc_final: 0.8058 (tp30) REVERT: f 177 GLU cc_start: 0.3195 (OUTLIER) cc_final: 0.2541 (pm20) REVERT: f 239 TYR cc_start: 0.8800 (m-80) cc_final: 0.8501 (m-10) REVERT: f 268 LEU cc_start: 0.9444 (mp) cc_final: 0.9083 (tt) REVERT: f 275 MET cc_start: 0.8061 (mtm) cc_final: 0.7320 (tmm) REVERT: f 294 MET cc_start: 0.7818 (ptp) cc_final: 0.6995 (ptt) REVERT: f 297 MET cc_start: 0.9152 (mtt) cc_final: 0.8845 (mtt) REVERT: f 309 GLU cc_start: 0.8480 (tp30) cc_final: 0.7731 (pm20) REVERT: f 340 MET cc_start: 0.6492 (mmm) cc_final: 0.6099 (mmm) REVERT: f 347 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8687 (p0) REVERT: f 416 MET cc_start: 0.8958 (mtm) cc_final: 0.8489 (mtm) REVERT: f 420 TRP cc_start: 0.7852 (m-10) cc_final: 0.7609 (m-90) REVERT: f 678 LEU cc_start: 0.9291 (mp) cc_final: 0.9021 (tt) REVERT: f 731 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8863 (tpp) REVERT: f 788 MET cc_start: 0.7968 (ptm) cc_final: 0.7357 (ttp) REVERT: f 796 LEU cc_start: 0.9246 (mm) cc_final: 0.9045 (mm) REVERT: f 830 LEU cc_start: 0.9266 (tp) cc_final: 0.9006 (tp) REVERT: g 93 LEU cc_start: 0.7575 (pp) cc_final: 0.6879 (mp) REVERT: g 133 LYS cc_start: 0.4759 (mmtt) cc_final: 0.4537 (mmtt) REVERT: g 159 LYS cc_start: 0.4147 (mmtm) cc_final: 0.3781 (mmmt) REVERT: u 178 TYR cc_start: 0.8683 (t80) cc_final: 0.8130 (t80) REVERT: u 218 LEU cc_start: 0.8625 (mt) cc_final: 0.8225 (tt) REVERT: u 266 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8565 (tp) outliers start: 342 outliers final: 194 residues processed: 1273 average time/residue: 0.6442 time to fit residues: 1406.1124 Evaluate side-chains 1099 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 884 time to evaluate : 6.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 313 ARG Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 351 LYS Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 163 HIS Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 235 GLN Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 98 GLU Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain U residue 185 MET Chi-restraints excluded: chain U residue 249 CYS Chi-restraints excluded: chain U residue 252 LEU Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain U residue 366 HIS Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 411 ILE Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 486 MET Chi-restraints excluded: chain U residue 552 ILE Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 675 MET Chi-restraints excluded: chain U residue 685 GLN Chi-restraints excluded: chain U residue 706 VAL Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 804 SER Chi-restraints excluded: chain U residue 835 ILE Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 78 HIS Chi-restraints excluded: chain V residue 135 LEU Chi-restraints excluded: chain V residue 144 ASP Chi-restraints excluded: chain V residue 147 PHE Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 194 LYS Chi-restraints excluded: chain V residue 205 LEU Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 230 PHE Chi-restraints excluded: chain V residue 249 THR Chi-restraints excluded: chain V residue 251 LEU Chi-restraints excluded: chain V residue 303 SER Chi-restraints excluded: chain V residue 334 VAL Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 392 TYR Chi-restraints excluded: chain V residue 394 LEU Chi-restraints excluded: chain V residue 400 HIS Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 308 LEU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 427 ASP Chi-restraints excluded: chain W residue 438 LEU Chi-restraints excluded: chain X residue 153 LEU Chi-restraints excluded: chain X residue 177 TYR Chi-restraints excluded: chain X residue 388 PHE Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 405 GLN Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 136 HIS Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Y residue 180 LEU Chi-restraints excluded: chain Y residue 220 VAL Chi-restraints excluded: chain Y residue 288 PHE Chi-restraints excluded: chain Y residue 330 ILE Chi-restraints excluded: chain Z residue 15 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 89 GLU Chi-restraints excluded: chain Z residue 108 ILE Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 135 THR Chi-restraints excluded: chain Z residue 182 THR Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 266 ILE Chi-restraints excluded: chain Z residue 270 VAL Chi-restraints excluded: chain Z residue 278 ASN Chi-restraints excluded: chain a residue 60 TYR Chi-restraints excluded: chain a residue 109 GLU Chi-restraints excluded: chain a residue 118 ILE Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 275 LEU Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 310 LEU Chi-restraints excluded: chain a residue 343 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 79 GLN Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 145 GLU Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 173 GLU Chi-restraints excluded: chain c residue 179 SER Chi-restraints excluded: chain c residue 181 LEU Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 205 ILE Chi-restraints excluded: chain c residue 218 LEU Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain d residue 118 ARG Chi-restraints excluded: chain d residue 198 PHE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 65 TYR Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 131 MET Chi-restraints excluded: chain f residue 177 GLU Chi-restraints excluded: chain f residue 256 PHE Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 446 LEU Chi-restraints excluded: chain f residue 485 LEU Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain f residue 552 ASP Chi-restraints excluded: chain f residue 731 MET Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 832 THR Chi-restraints excluded: chain f residue 905 ASN Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 167 ILE Chi-restraints excluded: chain u residue 182 PHE Chi-restraints excluded: chain u residue 244 VAL Chi-restraints excluded: chain u residue 266 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 379 optimal weight: 20.0000 chunk 817 optimal weight: 7.9990 chunk 544 optimal weight: 5.9990 chunk 863 optimal weight: 0.0370 chunk 154 optimal weight: 10.0000 chunk 604 optimal weight: 2.9990 chunk 623 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 436 optimal weight: 0.6980 chunk 267 optimal weight: 6.9990 chunk 474 optimal weight: 0.0970 overall best weight: 1.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 HIS D 49 GLN D 340 GLN E 32 GLN E 345 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 152 GLN U 89 ASN U 215 ASN ** U 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 388 ASN Z 7 GLN Z 22 HIS Z 235 ASN ** Z 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 131 GLN ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 183 HIS c 214 GLN ** d 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 747 GLN g 99 ASN ** g 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 160 GLN ** u 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 289 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.076486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.059382 restraints weight = 369773.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.061087 restraints weight = 204879.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.062197 restraints weight = 134680.477| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 71563 Z= 0.222 Angle : 0.759 12.357 96729 Z= 0.384 Chirality : 0.045 0.321 11063 Planarity : 0.005 0.072 12470 Dihedral : 7.765 147.688 9879 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.03 % Favored : 93.53 % Rotamer: Outliers : 4.11 % Allowed : 19.10 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.09), residues: 8837 helix: 0.40 (0.07), residues: 4801 sheet: -0.51 (0.16), residues: 932 loop : -1.12 (0.12), residues: 3104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP a 255 HIS 0.013 0.001 HIS U 754 PHE 0.033 0.002 PHE M 135 TYR 0.024 0.002 TYR U 246 ARG 0.012 0.001 ARG c 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1315 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 313 poor density : 1002 time to evaluate : 6.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8561 (t0) cc_final: 0.8336 (t0) REVERT: A 138 MET cc_start: 0.8310 (tpt) cc_final: 0.8016 (tpt) REVERT: A 187 LEU cc_start: 0.9750 (OUTLIER) cc_final: 0.9535 (pp) REVERT: A 299 MET cc_start: 0.8967 (tmm) cc_final: 0.8742 (ppp) REVERT: A 301 GLU cc_start: 0.8810 (tp30) cc_final: 0.8480 (tm-30) REVERT: A 307 ASP cc_start: 0.7994 (t0) cc_final: 0.7566 (t0) REVERT: A 337 LEU cc_start: 0.9479 (mt) cc_final: 0.9073 (mt) REVERT: B 65 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9473 (mp) REVERT: B 69 LYS cc_start: 0.9356 (tttp) cc_final: 0.9105 (mmmt) REVERT: B 75 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8657 (mm-30) REVERT: B 107 MET cc_start: 0.8639 (mpp) cc_final: 0.8397 (mpp) REVERT: B 114 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8125 (mt-10) REVERT: B 118 ASP cc_start: 0.8734 (p0) cc_final: 0.8450 (p0) REVERT: B 191 ASP cc_start: 0.8373 (p0) cc_final: 0.8047 (p0) REVERT: B 225 TYR cc_start: 0.8377 (p90) cc_final: 0.8076 (p90) REVERT: B 311 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.6787 (tp30) REVERT: B 329 MET cc_start: 0.9109 (mtm) cc_final: 0.8776 (mtm) REVERT: B 401 GLU cc_start: 0.8990 (tp30) cc_final: 0.8458 (tt0) REVERT: B 404 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9263 (mm) REVERT: B 405 MET cc_start: 0.8844 (mtp) cc_final: 0.8459 (mtp) REVERT: B 412 MET cc_start: 0.8564 (tpp) cc_final: 0.8343 (tpp) REVERT: C 62 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8631 (tm-30) REVERT: C 230 MET cc_start: 0.8403 (ttm) cc_final: 0.8182 (ptp) REVERT: C 273 MET cc_start: 0.8109 (mmm) cc_final: 0.7757 (mmm) REVERT: C 385 MET cc_start: 0.8793 (ptt) cc_final: 0.8584 (ptt) REVERT: C 391 MET cc_start: 0.8452 (ptm) cc_final: 0.7730 (ptm) REVERT: C 396 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8487 (mm-30) REVERT: C 399 MET cc_start: 0.7570 (mmp) cc_final: 0.7358 (mmm) REVERT: C 403 LYS cc_start: 0.5315 (OUTLIER) cc_final: 0.4999 (ptpp) REVERT: D 71 GLU cc_start: 0.8578 (tp30) cc_final: 0.8348 (tp30) REVERT: D 92 PHE cc_start: 0.9390 (t80) cc_final: 0.9140 (t80) REVERT: D 97 ASP cc_start: 0.8891 (t0) cc_final: 0.8653 (t0) REVERT: D 141 ASP cc_start: 0.8334 (t0) cc_final: 0.8098 (t0) REVERT: D 313 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6957 (ptp90) REVERT: D 359 ASP cc_start: 0.8046 (t0) cc_final: 0.7631 (p0) REVERT: E 171 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8779 (mm) REVERT: E 295 LEU cc_start: 0.8335 (mt) cc_final: 0.8086 (mt) REVERT: E 352 MET cc_start: 0.9194 (mmt) cc_final: 0.8989 (mmt) REVERT: F 53 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.7071 (pttt) REVERT: F 71 ASP cc_start: 0.8711 (m-30) cc_final: 0.8453 (m-30) REVERT: F 251 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8024 (pp) REVERT: F 310 MET cc_start: 0.9162 (ppp) cc_final: 0.8864 (ppp) REVERT: F 351 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8873 (mtmm) REVERT: F 421 MET cc_start: 0.8755 (mmm) cc_final: 0.8469 (mmm) REVERT: F 437 TYR cc_start: 0.7101 (m-10) cc_final: 0.6621 (m-10) REVERT: H 23 GLU cc_start: 0.9362 (mt-10) cc_final: 0.9103 (mp0) REVERT: H 70 LYS cc_start: 0.9090 (mtmt) cc_final: 0.8581 (tptt) REVERT: H 119 GLN cc_start: 0.9364 (tm-30) cc_final: 0.9160 (tp40) REVERT: H 165 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8578 (mmmt) REVERT: H 177 ARG cc_start: 0.8822 (tpp-160) cc_final: 0.8302 (tpm170) REVERT: I 72 MET cc_start: 0.7403 (tpp) cc_final: 0.7168 (mmt) REVERT: I 198 ASN cc_start: 0.7324 (t0) cc_final: 0.6656 (m-40) REVERT: J 15 HIS cc_start: 0.8255 (m90) cc_final: 0.7949 (m90) REVERT: J 114 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8803 (pp) REVERT: K 8 TYR cc_start: 0.1882 (m-80) cc_final: 0.1517 (m-10) REVERT: K 59 MET cc_start: 0.8148 (tpt) cc_final: 0.7742 (tpt) REVERT: K 107 MET cc_start: 0.5665 (mpp) cc_final: 0.5303 (mpp) REVERT: L 46 LEU cc_start: 0.4222 (OUTLIER) cc_final: 0.3988 (pp) REVERT: L 65 HIS cc_start: 0.6319 (OUTLIER) cc_final: 0.5951 (t70) REVERT: M 66 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6150 (mp) REVERT: M 150 MET cc_start: 0.8482 (tmm) cc_final: 0.8197 (tmm) REVERT: U 35 TRP cc_start: 0.8986 (p-90) cc_final: 0.8720 (p-90) REVERT: U 188 MET cc_start: 0.6704 (tpt) cc_final: 0.6384 (ppp) REVERT: U 220 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8873 (mt) REVERT: U 242 LEU cc_start: 0.8535 (mt) cc_final: 0.8308 (mt) REVERT: U 251 ASP cc_start: 0.8739 (m-30) cc_final: 0.7743 (t0) REVERT: U 556 MET cc_start: 0.7960 (tpt) cc_final: 0.7566 (tpt) REVERT: U 604 HIS cc_start: 0.9259 (OUTLIER) cc_final: 0.8311 (t70) REVERT: U 738 ASP cc_start: 0.8849 (m-30) cc_final: 0.8623 (m-30) REVERT: U 778 PHE cc_start: 0.9260 (m-80) cc_final: 0.8920 (m-80) REVERT: U 878 LEU cc_start: 0.7776 (mt) cc_final: 0.7520 (mt) REVERT: V 38 LYS cc_start: 0.9059 (mtmt) cc_final: 0.8761 (mtmm) REVERT: V 139 MET cc_start: 0.9055 (ptm) cc_final: 0.8464 (ppp) REVERT: V 168 GLN cc_start: 0.2926 (mm110) cc_final: 0.2002 (tp40) REVERT: V 176 MET cc_start: 0.8664 (tpp) cc_final: 0.8088 (tpt) REVERT: V 180 ARG cc_start: 0.8482 (mtt180) cc_final: 0.8150 (ptp-170) REVERT: V 494 MET cc_start: 0.8901 (mmm) cc_final: 0.8554 (tpt) REVERT: W 140 ILE cc_start: 0.9475 (OUTLIER) cc_final: 0.9253 (tt) REVERT: W 161 GLU cc_start: 0.9397 (mp0) cc_final: 0.9192 (pm20) REVERT: W 177 MET cc_start: 0.5327 (tpp) cc_final: 0.4923 (tpp) REVERT: W 190 MET cc_start: 0.9273 (mtt) cc_final: 0.8906 (mtm) REVERT: W 194 LEU cc_start: 0.9216 (mt) cc_final: 0.8997 (mt) REVERT: W 259 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: W 310 THR cc_start: 0.8865 (m) cc_final: 0.8624 (p) REVERT: W 425 LEU cc_start: 0.9695 (mp) cc_final: 0.9471 (mp) REVERT: X 140 THR cc_start: 0.9516 (OUTLIER) cc_final: 0.9304 (p) REVERT: X 162 ASP cc_start: 0.7861 (t0) cc_final: 0.7522 (t0) REVERT: X 270 LEU cc_start: 0.9402 (mm) cc_final: 0.9071 (mp) REVERT: X 301 ASP cc_start: 0.8662 (t0) cc_final: 0.8377 (t0) REVERT: X 315 ASP cc_start: 0.8252 (m-30) cc_final: 0.7991 (p0) REVERT: X 373 LYS cc_start: 0.8579 (mtpt) cc_final: 0.8378 (mtpt) REVERT: Y 59 LYS cc_start: 0.9052 (pttt) cc_final: 0.8728 (mmtt) REVERT: Z 44 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8535 (mm-40) REVERT: Z 88 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7556 (mmt180) REVERT: Z 261 TYR cc_start: 0.9315 (t80) cc_final: 0.8969 (t80) REVERT: a 26 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8310 (tm-30) REVERT: a 142 LEU cc_start: 0.9129 (tp) cc_final: 0.8764 (mt) REVERT: a 278 MET cc_start: 0.8995 (mmm) cc_final: 0.8713 (mmm) REVERT: a 281 THR cc_start: 0.8431 (p) cc_final: 0.7793 (t) REVERT: a 335 TRP cc_start: 0.7581 (t60) cc_final: 0.7366 (t60) REVERT: a 365 MET cc_start: 0.8559 (ptt) cc_final: 0.8339 (ptt) REVERT: b 1 MET cc_start: 0.3679 (mtp) cc_final: 0.1497 (tpt) REVERT: b 7 MET cc_start: 0.8838 (mmm) cc_final: 0.8457 (mmm) REVERT: b 16 MET cc_start: 0.8618 (tpp) cc_final: 0.8373 (tpp) REVERT: b 70 ARG cc_start: 0.9266 (tpp80) cc_final: 0.8803 (mmm160) REVERT: b 107 MET cc_start: 0.7363 (mmt) cc_final: 0.7072 (mmt) REVERT: c 107 MET cc_start: 0.8384 (ppp) cc_final: 0.8184 (ppp) REVERT: c 148 ILE cc_start: 0.8875 (pp) cc_final: 0.8590 (pt) REVERT: c 152 LYS cc_start: 0.8553 (mttt) cc_final: 0.8335 (mttt) REVERT: c 303 MET cc_start: 0.8631 (mmm) cc_final: 0.8410 (mmm) REVERT: d 94 MET cc_start: 0.8402 (ptm) cc_final: 0.8134 (ptm) REVERT: d 108 ASN cc_start: 0.8445 (t0) cc_final: 0.8221 (t0) REVERT: d 160 ASP cc_start: 0.8235 (t0) cc_final: 0.7858 (t0) REVERT: d 168 MET cc_start: 0.9338 (tpp) cc_final: 0.8989 (tpp) REVERT: d 194 LEU cc_start: 0.9100 (mt) cc_final: 0.8815 (mt) REVERT: d 242 ASN cc_start: 0.8532 (t0) cc_final: 0.8171 (m-40) REVERT: d 299 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8419 (mmm) REVERT: d 309 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7877 (p) REVERT: f 58 MET cc_start: 0.9355 (mmm) cc_final: 0.8782 (ptt) REVERT: f 177 GLU cc_start: 0.3173 (OUTLIER) cc_final: 0.2583 (pm20) REVERT: f 268 LEU cc_start: 0.9427 (mp) cc_final: 0.8933 (tt) REVERT: f 275 MET cc_start: 0.8075 (mtm) cc_final: 0.7340 (tmm) REVERT: f 294 MET cc_start: 0.7778 (ptp) cc_final: 0.6915 (ptt) REVERT: f 297 MET cc_start: 0.9144 (mtt) cc_final: 0.8806 (mtt) REVERT: f 309 GLU cc_start: 0.8454 (tp30) cc_final: 0.7711 (pm20) REVERT: f 340 MET cc_start: 0.6740 (mmm) cc_final: 0.6353 (mmm) REVERT: f 416 MET cc_start: 0.9006 (mtm) cc_final: 0.8635 (mtm) REVERT: f 678 LEU cc_start: 0.9204 (mp) cc_final: 0.8990 (tt) REVERT: f 731 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8776 (tpp) REVERT: f 788 MET cc_start: 0.7857 (ptm) cc_final: 0.7593 (ttp) REVERT: g 93 LEU cc_start: 0.6951 (pp) cc_final: 0.6478 (mp) REVERT: g 112 LEU cc_start: 0.8666 (tp) cc_final: 0.8435 (pp) REVERT: g 159 LYS cc_start: 0.4331 (mmtm) cc_final: 0.4046 (mmmt) REVERT: u 178 TYR cc_start: 0.8627 (t80) cc_final: 0.8026 (t80) REVERT: u 196 ILE cc_start: 0.9420 (mm) cc_final: 0.9033 (tp) REVERT: u 218 LEU cc_start: 0.8669 (mt) cc_final: 0.8356 (tt) REVERT: u 266 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8608 (tp) outliers start: 313 outliers final: 180 residues processed: 1236 average time/residue: 0.6555 time to fit residues: 1393.8061 Evaluate side-chains 1096 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 890 time to evaluate : 6.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 313 ARG Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 351 LYS Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 163 HIS Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 65 HIS Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 212 GLU Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 98 GLU Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain U residue 185 MET Chi-restraints excluded: chain U residue 220 LEU Chi-restraints excluded: chain U residue 249 CYS Chi-restraints excluded: chain U residue 252 LEU Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 366 HIS Chi-restraints excluded: chain U residue 367 THR Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 411 ILE Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 473 VAL Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 604 HIS Chi-restraints excluded: chain U residue 685 GLN Chi-restraints excluded: chain U residue 706 VAL Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 135 LEU Chi-restraints excluded: chain V residue 144 ASP Chi-restraints excluded: chain V residue 147 PHE Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 175 MET Chi-restraints excluded: chain V residue 194 LYS Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 230 PHE Chi-restraints excluded: chain V residue 249 THR Chi-restraints excluded: chain V residue 251 LEU Chi-restraints excluded: chain V residue 263 LEU Chi-restraints excluded: chain V residue 334 VAL Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 394 LEU Chi-restraints excluded: chain V residue 443 ARG Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 216 GLU Chi-restraints excluded: chain W residue 217 GLU Chi-restraints excluded: chain W residue 259 GLU Chi-restraints excluded: chain W residue 308 LEU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 427 ASP Chi-restraints excluded: chain W residue 438 LEU Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 177 TYR Chi-restraints excluded: chain X residue 256 LEU Chi-restraints excluded: chain X residue 388 PHE Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 136 HIS Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Y residue 180 LEU Chi-restraints excluded: chain Y residue 220 VAL Chi-restraints excluded: chain Y residue 388 ASN Chi-restraints excluded: chain Z residue 15 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 88 ARG Chi-restraints excluded: chain Z residue 108 ILE Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 135 THR Chi-restraints excluded: chain Z residue 182 THR Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 231 GLN Chi-restraints excluded: chain Z residue 234 PHE Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 266 ILE Chi-restraints excluded: chain Z residue 270 VAL Chi-restraints excluded: chain Z residue 278 ASN Chi-restraints excluded: chain a residue 60 TYR Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 275 LEU Chi-restraints excluded: chain a residue 310 LEU Chi-restraints excluded: chain a residue 343 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 84 ILE Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 179 SER Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 218 LEU Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain d residue 198 PHE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain e residue 65 TYR Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 131 MET Chi-restraints excluded: chain f residue 177 GLU Chi-restraints excluded: chain f residue 256 PHE Chi-restraints excluded: chain f residue 266 LEU Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain f residue 552 ASP Chi-restraints excluded: chain f residue 731 MET Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 829 MET Chi-restraints excluded: chain f residue 905 ASN Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 167 ILE Chi-restraints excluded: chain u residue 182 PHE Chi-restraints excluded: chain u residue 244 VAL Chi-restraints excluded: chain u residue 266 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 149 optimal weight: 10.0000 chunk 556 optimal weight: 5.9990 chunk 763 optimal weight: 8.9990 chunk 734 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 498 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 387 optimal weight: 5.9990 chunk 388 optimal weight: 10.0000 chunk 579 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 HIS H 148 GLN ** I 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 HIS L 53 GLN ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 415 HIS ** U 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 246 HIS X 268 GLN X 322 HIS X 405 GLN ** Y 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 7 GLN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 235 ASN Z 277 ASN ** a 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 219 ASN c 287 HIS ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 747 GLN ** f 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 160 GLN u 148 ASN u 289 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.071545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.054612 restraints weight = 388483.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.056703 restraints weight = 224519.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.057440 restraints weight = 133086.904| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 71563 Z= 0.334 Angle : 0.789 14.900 96729 Z= 0.403 Chirality : 0.046 0.334 11063 Planarity : 0.005 0.071 12470 Dihedral : 7.575 164.365 9864 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.70 % Favored : 92.86 % Rotamer: Outliers : 4.66 % Allowed : 19.84 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -0.38 (0.09), residues: 8837 helix: 0.43 (0.07), residues: 4818 sheet: -0.53 (0.16), residues: 929 loop : -1.12 (0.12), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP a 255 HIS 0.015 0.002 HIS U 754 PHE 0.035 0.002 PHE W 309 TYR 0.025 0.002 TYR E 40 ARG 0.012 0.001 ARG D 391 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 355 poor density : 907 time to evaluate : 6.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.8871 (tmm) cc_final: 0.8562 (ppp) REVERT: A 300 LEU cc_start: 0.9473 (mt) cc_final: 0.8875 (mt) REVERT: A 307 ASP cc_start: 0.8083 (t0) cc_final: 0.7667 (t0) REVERT: A 420 TYR cc_start: 0.4221 (OUTLIER) cc_final: 0.3618 (m-80) REVERT: B 69 LYS cc_start: 0.9329 (tttp) cc_final: 0.9063 (mmmt) REVERT: B 75 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8541 (mm-30) REVERT: B 92 GLN cc_start: 0.8577 (mt0) cc_final: 0.8322 (pm20) REVERT: B 114 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8115 (mt-10) REVERT: B 118 ASP cc_start: 0.8881 (p0) cc_final: 0.8625 (p0) REVERT: B 165 ASP cc_start: 0.9117 (m-30) cc_final: 0.8790 (t0) REVERT: B 183 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8339 (p) REVERT: B 191 ASP cc_start: 0.8520 (p0) cc_final: 0.8149 (p0) REVERT: B 220 LYS cc_start: 0.6843 (ttmt) cc_final: 0.6565 (ttmt) REVERT: B 225 TYR cc_start: 0.8409 (p90) cc_final: 0.8121 (p90) REVERT: B 329 MET cc_start: 0.9093 (mtm) cc_final: 0.8654 (mtm) REVERT: B 385 MET cc_start: 0.8033 (ppp) cc_final: 0.7412 (ppp) REVERT: B 401 GLU cc_start: 0.8984 (tp30) cc_final: 0.8473 (tt0) REVERT: B 404 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9339 (mm) REVERT: B 405 MET cc_start: 0.8892 (mtp) cc_final: 0.8567 (mtp) REVERT: B 412 MET cc_start: 0.8540 (tpp) cc_final: 0.8333 (tpp) REVERT: C 62 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8817 (tm-30) REVERT: C 80 MET cc_start: 0.8666 (mmm) cc_final: 0.8440 (mmt) REVERT: C 150 MET cc_start: 0.8563 (ptp) cc_final: 0.8331 (ptp) REVERT: C 273 MET cc_start: 0.8173 (mmm) cc_final: 0.7902 (mmm) REVERT: C 385 MET cc_start: 0.8793 (ptt) cc_final: 0.8521 (ptt) REVERT: C 391 MET cc_start: 0.8597 (ptm) cc_final: 0.7943 (ptm) REVERT: C 396 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8563 (mm-30) REVERT: C 399 MET cc_start: 0.7718 (mmp) cc_final: 0.6993 (mmp) REVERT: C 403 LYS cc_start: 0.5729 (OUTLIER) cc_final: 0.5499 (ptpp) REVERT: D 214 MET cc_start: 0.9151 (tpt) cc_final: 0.8883 (ttt) REVERT: E 258 MET cc_start: 0.8566 (tmm) cc_final: 0.8344 (tmm) REVERT: E 264 MET cc_start: 0.7950 (ppp) cc_final: 0.7748 (ppp) REVERT: E 295 LEU cc_start: 0.8355 (mt) cc_final: 0.7709 (mt) REVERT: E 352 MET cc_start: 0.9231 (mmt) cc_final: 0.8956 (mmt) REVERT: F 53 LYS cc_start: 0.6738 (OUTLIER) cc_final: 0.6344 (pttt) REVERT: F 71 ASP cc_start: 0.8642 (m-30) cc_final: 0.8358 (m-30) REVERT: F 310 MET cc_start: 0.9175 (ppp) cc_final: 0.8874 (ppp) REVERT: F 373 MET cc_start: 0.8433 (mtm) cc_final: 0.8044 (mmm) REVERT: F 421 MET cc_start: 0.8905 (mmm) cc_final: 0.8557 (mmm) REVERT: F 437 TYR cc_start: 0.7683 (m-10) cc_final: 0.7037 (m-10) REVERT: G 130 GLU cc_start: 0.7097 (tp30) cc_final: 0.6514 (pp20) REVERT: G 179 LEU cc_start: 0.8636 (mt) cc_final: 0.8434 (mt) REVERT: H 70 LYS cc_start: 0.9075 (mtmt) cc_final: 0.8589 (tptt) REVERT: H 119 GLN cc_start: 0.9337 (tm-30) cc_final: 0.9070 (tp40) REVERT: H 165 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8655 (mmmt) REVERT: H 166 ASN cc_start: 0.8327 (m110) cc_final: 0.7371 (t0) REVERT: H 177 ARG cc_start: 0.8900 (tpp-160) cc_final: 0.8357 (tpm170) REVERT: H 205 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6124 (pp20) REVERT: I 61 PHE cc_start: 0.6206 (m-80) cc_final: 0.5579 (t80) REVERT: I 72 MET cc_start: 0.7335 (tpp) cc_final: 0.7038 (mmt) REVERT: I 198 ASN cc_start: 0.7460 (t0) cc_final: 0.6652 (m-40) REVERT: J 15 HIS cc_start: 0.8392 (m90) cc_final: 0.8072 (m90) REVERT: K 8 TYR cc_start: 0.2981 (m-80) cc_final: 0.2603 (m-10) REVERT: K 59 MET cc_start: 0.7865 (tpt) cc_final: 0.7555 (tpt) REVERT: K 156 MET cc_start: 0.7326 (ppp) cc_final: 0.6889 (ppp) REVERT: K 236 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6732 (pm20) REVERT: L 46 LEU cc_start: 0.4276 (OUTLIER) cc_final: 0.3929 (pp) REVERT: L 196 ARG cc_start: 0.4160 (OUTLIER) cc_final: 0.3699 (ttm-80) REVERT: M 17 ASP cc_start: 0.8733 (m-30) cc_final: 0.8091 (t70) REVERT: M 66 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.5335 (mt) REVERT: M 136 MET cc_start: 0.3980 (ttt) cc_final: 0.3423 (ttt) REVERT: U 35 TRP cc_start: 0.8978 (p-90) cc_final: 0.8711 (p-90) REVERT: U 182 LYS cc_start: 0.9478 (tppt) cc_final: 0.9243 (tppt) REVERT: U 188 MET cc_start: 0.7129 (tpt) cc_final: 0.6565 (ppp) REVERT: U 190 ASN cc_start: 0.8779 (m-40) cc_final: 0.8242 (p0) REVERT: U 220 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8963 (mt) REVERT: U 556 MET cc_start: 0.8267 (tpt) cc_final: 0.7840 (tpt) REVERT: U 604 HIS cc_start: 0.9255 (OUTLIER) cc_final: 0.8061 (t70) REVERT: U 694 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8462 (tt) REVERT: U 738 ASP cc_start: 0.8791 (m-30) cc_final: 0.8556 (m-30) REVERT: U 906 LEU cc_start: 0.7723 (tp) cc_final: 0.7254 (tp) REVERT: V 38 LYS cc_start: 0.9111 (mtmt) cc_final: 0.8844 (mtmm) REVERT: V 139 MET cc_start: 0.9092 (ptm) cc_final: 0.8531 (ppp) REVERT: V 176 MET cc_start: 0.8745 (tpp) cc_final: 0.8057 (tpt) REVERT: V 180 ARG cc_start: 0.8664 (mtt180) cc_final: 0.8322 (ptp-170) REVERT: V 245 ASP cc_start: 0.8401 (m-30) cc_final: 0.8061 (m-30) REVERT: V 301 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8065 (tm-30) REVERT: V 358 MET cc_start: 0.8430 (tmm) cc_final: 0.8148 (tmm) REVERT: V 494 MET cc_start: 0.8819 (mmm) cc_final: 0.8512 (tpt) REVERT: W 123 ARG cc_start: 0.8869 (mmp-170) cc_final: 0.8187 (mmt180) REVERT: W 140 ILE cc_start: 0.9493 (OUTLIER) cc_final: 0.9251 (tt) REVERT: W 177 MET cc_start: 0.5766 (tpp) cc_final: 0.5402 (tpp) REVERT: W 200 ILE cc_start: 0.9255 (mp) cc_final: 0.9015 (pt) REVERT: W 310 THR cc_start: 0.8901 (m) cc_final: 0.8619 (p) REVERT: X 140 THR cc_start: 0.9523 (OUTLIER) cc_final: 0.9244 (p) REVERT: X 162 ASP cc_start: 0.7829 (t0) cc_final: 0.7396 (t0) REVERT: X 301 ASP cc_start: 0.8672 (t0) cc_final: 0.8350 (t70) REVERT: Y 59 LYS cc_start: 0.9165 (pttt) cc_final: 0.8913 (mmtt) REVERT: Y 282 MET cc_start: 0.9019 (tpp) cc_final: 0.8295 (tpp) REVERT: Y 288 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8292 (t80) REVERT: Z 44 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8507 (mm-40) REVERT: Z 68 TRP cc_start: 0.8527 (p-90) cc_final: 0.7983 (p-90) REVERT: Z 165 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8424 (tm-30) REVERT: Z 261 TYR cc_start: 0.9378 (t80) cc_final: 0.8987 (t80) REVERT: a 34 TRP cc_start: 0.7737 (m-90) cc_final: 0.7475 (m-90) REVERT: a 109 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6560 (tp30) REVERT: a 141 MET cc_start: 0.8515 (ppp) cc_final: 0.8059 (ppp) REVERT: a 142 LEU cc_start: 0.9148 (tp) cc_final: 0.8756 (mt) REVERT: a 312 MET cc_start: 0.9188 (mtm) cc_final: 0.8887 (mtm) REVERT: b 1 MET cc_start: 0.4382 (mtp) cc_final: 0.1669 (tpt) REVERT: d 108 ASN cc_start: 0.8697 (t0) cc_final: 0.8492 (t0) REVERT: d 160 ASP cc_start: 0.8466 (t0) cc_final: 0.8124 (t0) REVERT: d 168 MET cc_start: 0.9406 (tpp) cc_final: 0.9057 (tpp) REVERT: d 215 LEU cc_start: 0.8908 (mm) cc_final: 0.8619 (mm) REVERT: d 299 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8494 (mmm) REVERT: d 309 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.8000 (p) REVERT: f 177 GLU cc_start: 0.3060 (OUTLIER) cc_final: 0.2575 (pm20) REVERT: f 275 MET cc_start: 0.8225 (mtm) cc_final: 0.7535 (tmm) REVERT: f 294 MET cc_start: 0.7805 (ptp) cc_final: 0.6926 (ptt) REVERT: f 297 MET cc_start: 0.9106 (mtt) cc_final: 0.8753 (mtt) REVERT: f 309 GLU cc_start: 0.8430 (tp30) cc_final: 0.7585 (pm20) REVERT: f 340 MET cc_start: 0.7095 (mmm) cc_final: 0.6688 (mmm) REVERT: f 416 MET cc_start: 0.9026 (mtm) cc_final: 0.8661 (mtm) REVERT: f 485 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8609 (pp) REVERT: f 731 MET cc_start: 0.9108 (tpt) cc_final: 0.8900 (tpp) REVERT: f 744 MET cc_start: 0.9410 (mtt) cc_final: 0.9164 (mtt) REVERT: f 784 ASP cc_start: 0.8443 (t0) cc_final: 0.8048 (t70) REVERT: f 788 MET cc_start: 0.8135 (ptm) cc_final: 0.7740 (ttp) REVERT: f 829 MET cc_start: 0.8131 (pmm) cc_final: 0.7625 (pmm) REVERT: g 94 LYS cc_start: 0.7545 (mmtp) cc_final: 0.7340 (mppt) REVERT: g 159 LYS cc_start: 0.4502 (mmtm) cc_final: 0.4213 (mmmt) REVERT: u 178 TYR cc_start: 0.8762 (t80) cc_final: 0.8169 (t80) REVERT: u 266 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8613 (tp) outliers start: 355 outliers final: 221 residues processed: 1176 average time/residue: 0.6748 time to fit residues: 1358.1891 Evaluate side-chains 1057 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 813 time to evaluate : 6.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 420 TYR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 351 LYS Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain G residue 23 TYR Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 228 ARG Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 163 HIS Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain L residue 196 ARG Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 165 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 98 GLU Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain U residue 146 LYS Chi-restraints excluded: chain U residue 185 MET Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain U residue 220 LEU Chi-restraints excluded: chain U residue 249 CYS Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 366 HIS Chi-restraints excluded: chain U residue 367 THR Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 411 ILE Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 473 VAL Chi-restraints excluded: chain U residue 552 ILE Chi-restraints excluded: chain U residue 593 SER Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 604 HIS Chi-restraints excluded: chain U residue 694 ILE Chi-restraints excluded: chain U residue 706 VAL Chi-restraints excluded: chain U residue 711 GLN Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 804 SER Chi-restraints excluded: chain U residue 835 ILE Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 135 LEU Chi-restraints excluded: chain V residue 144 ASP Chi-restraints excluded: chain V residue 147 PHE Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 175 MET Chi-restraints excluded: chain V residue 194 LYS Chi-restraints excluded: chain V residue 205 LEU Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 230 PHE Chi-restraints excluded: chain V residue 249 THR Chi-restraints excluded: chain V residue 263 LEU Chi-restraints excluded: chain V residue 270 LEU Chi-restraints excluded: chain V residue 334 VAL Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 363 LEU Chi-restraints excluded: chain V residue 392 TYR Chi-restraints excluded: chain V residue 394 LEU Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain V residue 443 ARG Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 216 GLU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 427 ASP Chi-restraints excluded: chain W residue 438 LEU Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 177 TYR Chi-restraints excluded: chain X residue 388 PHE Chi-restraints excluded: chain X residue 414 LEU Chi-restraints excluded: chain X residue 416 ASN Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 136 HIS Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Y residue 180 LEU Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 220 VAL Chi-restraints excluded: chain Y residue 288 PHE Chi-restraints excluded: chain Z residue 15 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 72 HIS Chi-restraints excluded: chain Z residue 92 VAL Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 135 THR Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 182 THR Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 231 GLN Chi-restraints excluded: chain Z residue 234 PHE Chi-restraints excluded: chain Z residue 240 VAL Chi-restraints excluded: chain Z residue 266 ILE Chi-restraints excluded: chain Z residue 270 VAL Chi-restraints excluded: chain Z residue 278 ASN Chi-restraints excluded: chain a residue 60 TYR Chi-restraints excluded: chain a residue 99 LYS Chi-restraints excluded: chain a residue 109 GLU Chi-restraints excluded: chain a residue 118 ILE Chi-restraints excluded: chain a residue 138 VAL Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 275 LEU Chi-restraints excluded: chain a residue 296 ILE Chi-restraints excluded: chain a residue 310 LEU Chi-restraints excluded: chain a residue 343 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 58 CYS Chi-restraints excluded: chain b residue 84 ILE Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 183 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 179 SER Chi-restraints excluded: chain c residue 181 LEU Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 218 LEU Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 282 ARG Chi-restraints excluded: chain d residue 198 PHE Chi-restraints excluded: chain d residue 245 PHE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain e residue 65 TYR Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 131 MET Chi-restraints excluded: chain f residue 177 GLU Chi-restraints excluded: chain f residue 256 PHE Chi-restraints excluded: chain f residue 266 LEU Chi-restraints excluded: chain f residue 346 ASP Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 485 LEU Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 832 THR Chi-restraints excluded: chain f residue 852 VAL Chi-restraints excluded: chain f residue 905 ASN Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 167 ILE Chi-restraints excluded: chain u residue 182 PHE Chi-restraints excluded: chain u residue 241 VAL Chi-restraints excluded: chain u residue 244 VAL Chi-restraints excluded: chain u residue 266 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 348 optimal weight: 7.9990 chunk 723 optimal weight: 3.9990 chunk 361 optimal weight: 0.7980 chunk 356 optimal weight: 30.0000 chunk 216 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 546 optimal weight: 3.9990 chunk 832 optimal weight: 0.5980 chunk 641 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 HIS ** L 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 347 GLN W 235 GLN W 430 GLN ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 273 GLN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 130 GLN ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 747 GLN f 758 ASN ** g 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 160 GLN ** u 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 289 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.072514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.055646 restraints weight = 381970.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.057863 restraints weight = 213376.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.058530 restraints weight = 126870.051| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.6520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 71563 Z= 0.226 Angle : 0.753 17.803 96729 Z= 0.376 Chirality : 0.045 0.356 11063 Planarity : 0.005 0.074 12470 Dihedral : 7.295 160.782 9858 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.93 % Favored : 93.64 % Rotamer: Outliers : 3.84 % Allowed : 21.39 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -0.25 (0.09), residues: 8837 helix: 0.60 (0.08), residues: 4822 sheet: -0.63 (0.17), residues: 925 loop : -1.12 (0.12), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP a 255 HIS 0.013 0.001 HIS U 754 PHE 0.030 0.002 PHE Z 69 TYR 0.031 0.002 TYR W 75 ARG 0.010 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 292 poor density : 921 time to evaluate : 6.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8204 (tpt) cc_final: 0.8002 (tpt) REVERT: A 300 LEU cc_start: 0.9470 (mt) cc_final: 0.8917 (mt) REVERT: A 301 GLU cc_start: 0.8894 (tp30) cc_final: 0.8564 (tm-30) REVERT: A 307 ASP cc_start: 0.8020 (t0) cc_final: 0.7569 (t0) REVERT: B 69 LYS cc_start: 0.9313 (tttp) cc_final: 0.9093 (mmmt) REVERT: B 75 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8471 (mm-30) REVERT: B 92 GLN cc_start: 0.8490 (mt0) cc_final: 0.8195 (pm20) REVERT: B 114 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8001 (mt-10) REVERT: B 118 ASP cc_start: 0.8786 (p0) cc_final: 0.8556 (p0) REVERT: B 183 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8230 (p) REVERT: B 191 ASP cc_start: 0.8517 (p0) cc_final: 0.8133 (p0) REVERT: B 220 LYS cc_start: 0.6824 (ttmt) cc_final: 0.6600 (ttmt) REVERT: B 225 TYR cc_start: 0.8350 (p90) cc_final: 0.8082 (p90) REVERT: B 329 MET cc_start: 0.9085 (mtm) cc_final: 0.8725 (mtm) REVERT: B 401 GLU cc_start: 0.8954 (tp30) cc_final: 0.8423 (tt0) REVERT: B 404 LEU cc_start: 0.9673 (OUTLIER) cc_final: 0.9331 (mm) REVERT: B 405 MET cc_start: 0.8897 (mtp) cc_final: 0.8552 (mtp) REVERT: B 412 MET cc_start: 0.8454 (tpp) cc_final: 0.8234 (tpp) REVERT: C 62 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8687 (tm-30) REVERT: C 80 MET cc_start: 0.8703 (mmm) cc_final: 0.8457 (mmt) REVERT: C 81 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8266 (p0) REVERT: C 273 MET cc_start: 0.8116 (mmm) cc_final: 0.7808 (mmm) REVERT: C 369 TYR cc_start: 0.8965 (m-10) cc_final: 0.8628 (m-10) REVERT: C 385 MET cc_start: 0.8852 (ptt) cc_final: 0.8532 (ptt) REVERT: C 391 MET cc_start: 0.8635 (ptm) cc_final: 0.7960 (ptm) REVERT: C 396 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8622 (mm-30) REVERT: C 399 MET cc_start: 0.7884 (mmp) cc_final: 0.7351 (mmp) REVERT: C 403 LYS cc_start: 0.5549 (OUTLIER) cc_final: 0.5049 (ptpp) REVERT: D 60 TYR cc_start: 0.9144 (OUTLIER) cc_final: 0.8475 (t80) REVERT: D 71 GLU cc_start: 0.8757 (tp30) cc_final: 0.8502 (tp30) REVERT: D 97 ASP cc_start: 0.8968 (t0) cc_final: 0.8644 (t0) REVERT: D 98 GLN cc_start: 0.8786 (mp10) cc_final: 0.8499 (mp10) REVERT: D 214 MET cc_start: 0.9224 (tpt) cc_final: 0.9019 (ttt) REVERT: D 287 ARG cc_start: 0.9058 (mtm-85) cc_final: 0.8807 (mtm-85) REVERT: D 356 GLU cc_start: 0.9148 (tp30) cc_final: 0.8830 (pm20) REVERT: E 258 MET cc_start: 0.8539 (tmm) cc_final: 0.8279 (tmm) REVERT: E 295 LEU cc_start: 0.8266 (mt) cc_final: 0.8050 (mt) REVERT: E 352 MET cc_start: 0.9177 (mmt) cc_final: 0.8973 (mmt) REVERT: F 53 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6540 (pttt) REVERT: F 61 ARG cc_start: 0.7318 (mtm180) cc_final: 0.7000 (mtm180) REVERT: F 71 ASP cc_start: 0.8673 (m-30) cc_final: 0.8426 (m-30) REVERT: F 310 MET cc_start: 0.9154 (ppp) cc_final: 0.8832 (ppp) REVERT: F 351 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8554 (mtmt) REVERT: F 373 MET cc_start: 0.8382 (mtm) cc_final: 0.8145 (mmm) REVERT: F 421 MET cc_start: 0.8902 (mmm) cc_final: 0.8601 (mmm) REVERT: F 437 TYR cc_start: 0.7601 (m-10) cc_final: 0.6940 (m-10) REVERT: G 80 MET cc_start: 0.7268 (mmm) cc_final: 0.6165 (mmm) REVERT: G 130 GLU cc_start: 0.7136 (tp30) cc_final: 0.6629 (pp20) REVERT: H 70 LYS cc_start: 0.9037 (mtmt) cc_final: 0.8561 (tptt) REVERT: H 74 LEU cc_start: 0.8913 (tp) cc_final: 0.8668 (tp) REVERT: H 119 GLN cc_start: 0.9362 (tm-30) cc_final: 0.9107 (tp40) REVERT: H 166 ASN cc_start: 0.8301 (m110) cc_final: 0.7428 (t0) REVERT: H 177 ARG cc_start: 0.8898 (tpp-160) cc_final: 0.8381 (tpm170) REVERT: I 61 PHE cc_start: 0.6198 (m-80) cc_final: 0.5572 (t80) REVERT: I 72 MET cc_start: 0.7386 (tpp) cc_final: 0.7151 (mmt) REVERT: I 198 ASN cc_start: 0.7433 (t0) cc_final: 0.6676 (m-40) REVERT: J 15 HIS cc_start: 0.8298 (m90) cc_final: 0.8002 (m90) REVERT: K 8 TYR cc_start: 0.2735 (m-80) cc_final: 0.2401 (m-10) REVERT: K 59 MET cc_start: 0.7593 (tpt) cc_final: 0.7044 (tpt) REVERT: K 81 LEU cc_start: 0.8601 (tp) cc_final: 0.8164 (tt) REVERT: K 156 MET cc_start: 0.7358 (ppp) cc_final: 0.7053 (ppp) REVERT: K 206 MET cc_start: 0.7017 (mmt) cc_final: 0.6788 (mmt) REVERT: K 225 ASN cc_start: 0.9007 (m-40) cc_final: 0.8769 (t0) REVERT: L 46 LEU cc_start: 0.4340 (OUTLIER) cc_final: 0.3939 (pp) REVERT: M 17 ASP cc_start: 0.8715 (m-30) cc_final: 0.8026 (t70) REVERT: M 66 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.5926 (mt) REVERT: U 35 TRP cc_start: 0.8935 (p-90) cc_final: 0.8678 (p-90) REVERT: U 176 MET cc_start: 0.7712 (mmt) cc_final: 0.7448 (tpt) REVERT: U 179 TYR cc_start: 0.8854 (t80) cc_final: 0.8489 (t80) REVERT: U 188 MET cc_start: 0.7136 (tpt) cc_final: 0.6403 (ppp) REVERT: U 190 ASN cc_start: 0.8731 (m-40) cc_final: 0.8315 (p0) REVERT: U 520 MET cc_start: 0.8737 (mmm) cc_final: 0.8146 (mmm) REVERT: U 604 HIS cc_start: 0.9219 (OUTLIER) cc_final: 0.8021 (t70) REVERT: U 694 ILE cc_start: 0.8717 (tt) cc_final: 0.8453 (tt) REVERT: U 738 ASP cc_start: 0.8730 (m-30) cc_final: 0.8121 (t0) REVERT: U 757 MET cc_start: 0.8623 (tmm) cc_final: 0.8360 (tmm) REVERT: U 906 LEU cc_start: 0.7936 (tp) cc_final: 0.7557 (tp) REVERT: V 38 LYS cc_start: 0.9070 (mtmt) cc_final: 0.8772 (mtmm) REVERT: V 139 MET cc_start: 0.9057 (ptm) cc_final: 0.8490 (ppp) REVERT: V 180 ARG cc_start: 0.8647 (mtt180) cc_final: 0.8290 (ptp-170) REVERT: V 299 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8301 (tm-30) REVERT: V 301 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7864 (tm-30) REVERT: V 344 ASP cc_start: 0.7062 (t0) cc_final: 0.6716 (t70) REVERT: V 358 MET cc_start: 0.8406 (tmm) cc_final: 0.8081 (tmm) REVERT: V 482 PHE cc_start: 0.8890 (t80) cc_final: 0.8523 (t80) REVERT: V 494 MET cc_start: 0.8727 (mmm) cc_final: 0.8481 (tpt) REVERT: W 200 ILE cc_start: 0.9275 (mp) cc_final: 0.9030 (pt) REVERT: X 140 THR cc_start: 0.9522 (OUTLIER) cc_final: 0.9254 (p) REVERT: X 162 ASP cc_start: 0.7908 (t0) cc_final: 0.7520 (t0) REVERT: X 270 LEU cc_start: 0.9567 (mm) cc_final: 0.9295 (mm) REVERT: X 301 ASP cc_start: 0.8714 (t0) cc_final: 0.8361 (t0) REVERT: Y 59 LYS cc_start: 0.9129 (pttt) cc_final: 0.8849 (mmtt) REVERT: Y 250 LEU cc_start: 0.9486 (mt) cc_final: 0.9224 (mt) REVERT: Y 293 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7898 (mmt180) REVERT: Z 44 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8423 (mm-40) REVERT: Z 68 TRP cc_start: 0.8476 (p-90) cc_final: 0.8032 (p-90) REVERT: Z 229 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7716 (tm-30) REVERT: Z 261 TYR cc_start: 0.9340 (t80) cc_final: 0.8997 (t80) REVERT: a 141 MET cc_start: 0.8513 (ppp) cc_final: 0.8051 (ppp) REVERT: a 142 LEU cc_start: 0.9069 (tp) cc_final: 0.8655 (mt) REVERT: a 312 MET cc_start: 0.9116 (mtm) cc_final: 0.8807 (mtm) REVERT: a 365 MET cc_start: 0.8562 (ptt) cc_final: 0.8290 (ptt) REVERT: b 1 MET cc_start: 0.4454 (mtp) cc_final: 0.1604 (tpt) REVERT: b 7 MET cc_start: 0.8905 (tpp) cc_final: 0.8694 (tpt) REVERT: b 15 TYR cc_start: 0.9073 (m-80) cc_final: 0.8424 (m-80) REVERT: b 16 MET cc_start: 0.8644 (tpp) cc_final: 0.8350 (tpp) REVERT: b 85 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.9021 (p) REVERT: c 289 ASP cc_start: 0.8866 (t0) cc_final: 0.8660 (t0) REVERT: d 108 ASN cc_start: 0.8620 (t0) cc_final: 0.8409 (t0) REVERT: d 160 ASP cc_start: 0.8602 (t0) cc_final: 0.8283 (t0) REVERT: d 168 MET cc_start: 0.9381 (tpp) cc_final: 0.9045 (tpp) REVERT: d 194 LEU cc_start: 0.9167 (mt) cc_final: 0.8945 (mt) REVERT: d 299 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8582 (mmm) REVERT: d 309 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8011 (p) REVERT: f 58 MET cc_start: 0.9401 (mmm) cc_final: 0.9015 (ppp) REVERT: f 177 GLU cc_start: 0.2866 (OUTLIER) cc_final: 0.2243 (pm20) REVERT: f 275 MET cc_start: 0.8295 (mtm) cc_final: 0.7662 (tmm) REVERT: f 294 MET cc_start: 0.7811 (ptp) cc_final: 0.6949 (ptt) REVERT: f 297 MET cc_start: 0.9118 (mtt) cc_final: 0.8756 (mtt) REVERT: f 309 GLU cc_start: 0.8434 (tp30) cc_final: 0.7570 (pm20) REVERT: f 313 GLU cc_start: 0.7532 (mp0) cc_final: 0.7218 (mp0) REVERT: f 340 MET cc_start: 0.7365 (mmm) cc_final: 0.7006 (mmm) REVERT: f 416 MET cc_start: 0.9003 (mtm) cc_final: 0.8626 (mtm) REVERT: f 477 MET cc_start: 0.8526 (mmm) cc_final: 0.6692 (tpt) REVERT: f 524 MET cc_start: 0.8684 (ptt) cc_final: 0.8348 (ptt) REVERT: f 543 MET cc_start: 0.6888 (tpp) cc_final: 0.6601 (mmm) REVERT: f 670 MET cc_start: 0.8962 (mmp) cc_final: 0.8758 (mmm) REVERT: f 744 MET cc_start: 0.9443 (mtt) cc_final: 0.9169 (mtt) REVERT: f 784 ASP cc_start: 0.8273 (t0) cc_final: 0.7912 (t70) REVERT: g 159 LYS cc_start: 0.4422 (mmtm) cc_final: 0.4149 (mmmt) REVERT: u 178 TYR cc_start: 0.8705 (t80) cc_final: 0.8053 (t80) REVERT: u 180 MET cc_start: 0.8744 (ppp) cc_final: 0.8540 (tmm) REVERT: u 266 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8611 (tp) REVERT: u 285 LYS cc_start: 0.7745 (mttt) cc_final: 0.7276 (mmmt) outliers start: 292 outliers final: 185 residues processed: 1135 average time/residue: 0.6533 time to fit residues: 1269.7851 Evaluate side-chains 1037 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 834 time to evaluate : 6.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 351 LYS Chi-restraints excluded: chain G residue 23 TYR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 163 HIS Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 165 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain U residue 146 LYS Chi-restraints excluded: chain U residue 249 CYS Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 366 HIS Chi-restraints excluded: chain U residue 367 THR Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 411 ILE Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 462 LEU Chi-restraints excluded: chain U residue 552 ILE Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 604 HIS Chi-restraints excluded: chain U residue 685 GLN Chi-restraints excluded: chain U residue 706 VAL Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 835 ILE Chi-restraints excluded: chain U residue 921 ILE Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 135 LEU Chi-restraints excluded: chain V residue 144 ASP Chi-restraints excluded: chain V residue 147 PHE Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 175 MET Chi-restraints excluded: chain V residue 194 LYS Chi-restraints excluded: chain V residue 212 TYR Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 230 PHE Chi-restraints excluded: chain V residue 263 LEU Chi-restraints excluded: chain V residue 334 VAL Chi-restraints excluded: chain V residue 394 LEU Chi-restraints excluded: chain V residue 422 ILE Chi-restraints excluded: chain V residue 443 ARG Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 216 GLU Chi-restraints excluded: chain W residue 217 GLU Chi-restraints excluded: chain W residue 351 TRP Chi-restraints excluded: chain W residue 427 ASP Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 177 TYR Chi-restraints excluded: chain X residue 256 LEU Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 388 PHE Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 414 LEU Chi-restraints excluded: chain X residue 416 ASN Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 136 HIS Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Y residue 180 LEU Chi-restraints excluded: chain Y residue 220 VAL Chi-restraints excluded: chain Y residue 293 ARG Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 72 HIS Chi-restraints excluded: chain Z residue 92 VAL Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 135 THR Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 182 THR Chi-restraints excluded: chain Z residue 195 VAL Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 231 GLN Chi-restraints excluded: chain Z residue 234 PHE Chi-restraints excluded: chain Z residue 270 VAL Chi-restraints excluded: chain Z residue 278 ASN Chi-restraints excluded: chain a residue 60 TYR Chi-restraints excluded: chain a residue 138 VAL Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 310 LEU Chi-restraints excluded: chain a residue 343 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 84 ILE Chi-restraints excluded: chain b residue 85 THR Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 118 PHE Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 179 SER Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 218 LEU Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain d residue 198 PHE Chi-restraints excluded: chain d residue 219 ASP Chi-restraints excluded: chain d residue 242 ASN Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain d residue 326 GLU Chi-restraints excluded: chain d residue 348 MET Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 177 GLU Chi-restraints excluded: chain f residue 256 PHE Chi-restraints excluded: chain f residue 266 LEU Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 573 ILE Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 852 VAL Chi-restraints excluded: chain f residue 905 ASN Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 167 ILE Chi-restraints excluded: chain u residue 182 PHE Chi-restraints excluded: chain u residue 244 VAL Chi-restraints excluded: chain u residue 266 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 504 optimal weight: 10.0000 chunk 233 optimal weight: 30.0000 chunk 451 optimal weight: 8.9990 chunk 290 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 524 optimal weight: 0.9990 chunk 760 optimal weight: 9.9990 chunk 333 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 680 optimal weight: 5.9990 chunk 776 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 HIS ** U 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 86 ASN ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 7 GLN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN Z 145 HIS Z 224 HIS ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 HIS ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 130 GLN d 228 HIS ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 102 HIS ** f 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 747 GLN ** f 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 160 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.083665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.066641 restraints weight = 372752.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.068235 restraints weight = 204402.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.069233 restraints weight = 134120.166| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.6982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 71563 Z= 0.320 Angle : 0.792 17.766 96729 Z= 0.398 Chirality : 0.045 0.271 11063 Planarity : 0.005 0.074 12470 Dihedral : 7.306 169.518 9853 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.73 % Favored : 92.87 % Rotamer: Outliers : 4.03 % Allowed : 21.91 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -0.27 (0.09), residues: 8837 helix: 0.58 (0.08), residues: 4809 sheet: -0.79 (0.16), residues: 929 loop : -1.06 (0.12), residues: 3099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP a 335 HIS 0.014 0.002 HIS U 754 PHE 0.030 0.002 PHE L 179 TYR 0.035 0.002 TYR W 75 ARG 0.010 0.001 ARG b 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 307 poor density : 829 time to evaluate : 6.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.7945 (t0) REVERT: A 307 ASP cc_start: 0.8245 (t0) cc_final: 0.7483 (t0) REVERT: A 333 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7914 (ttt90) REVERT: A 420 TYR cc_start: 0.4469 (OUTLIER) cc_final: 0.3817 (m-80) REVERT: B 69 LYS cc_start: 0.9342 (tttp) cc_final: 0.9082 (mmmt) REVERT: B 75 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8555 (mm-30) REVERT: B 92 GLN cc_start: 0.8458 (mt0) cc_final: 0.8219 (pm20) REVERT: B 114 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8083 (mt-10) REVERT: B 183 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8368 (p) REVERT: B 225 TYR cc_start: 0.8471 (p90) cc_final: 0.8215 (p90) REVERT: B 329 MET cc_start: 0.9006 (mtm) cc_final: 0.8623 (mtm) REVERT: B 404 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9322 (mm) REVERT: B 405 MET cc_start: 0.9068 (mtp) cc_final: 0.8711 (mtp) REVERT: C 62 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8752 (tm-30) REVERT: C 273 MET cc_start: 0.8311 (mmm) cc_final: 0.8005 (mmm) REVERT: C 391 MET cc_start: 0.8566 (ptm) cc_final: 0.8088 (ptm) REVERT: C 396 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8580 (mm-30) REVERT: C 399 MET cc_start: 0.7708 (mmp) cc_final: 0.7241 (mmp) REVERT: C 403 LYS cc_start: 0.5915 (OUTLIER) cc_final: 0.5387 (ptpp) REVERT: D 60 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.8707 (t80) REVERT: D 71 GLU cc_start: 0.8767 (tp30) cc_final: 0.8429 (tp30) REVERT: D 97 ASP cc_start: 0.9025 (t0) cc_final: 0.8733 (t70) REVERT: D 98 GLN cc_start: 0.8844 (mp10) cc_final: 0.8626 (mp10) REVERT: D 192 LYS cc_start: 0.9276 (ttpt) cc_final: 0.8951 (mttt) REVERT: D 214 MET cc_start: 0.9195 (tpt) cc_final: 0.8908 (ttp) REVERT: D 287 ARG cc_start: 0.9061 (mtm-85) cc_final: 0.8689 (mtt-85) REVERT: D 356 GLU cc_start: 0.9248 (tp30) cc_final: 0.8830 (pm20) REVERT: E 258 MET cc_start: 0.8435 (tmm) cc_final: 0.8228 (tmm) REVERT: E 352 MET cc_start: 0.9253 (mmt) cc_final: 0.9000 (mmt) REVERT: F 53 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6660 (pttt) REVERT: F 71 ASP cc_start: 0.8505 (m-30) cc_final: 0.8216 (m-30) REVERT: F 310 MET cc_start: 0.9070 (ppp) cc_final: 0.8659 (ppp) REVERT: F 316 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8616 (mm110) REVERT: F 421 MET cc_start: 0.8968 (mmm) cc_final: 0.8644 (mmm) REVERT: F 437 TYR cc_start: 0.7446 (m-10) cc_final: 0.6794 (m-10) REVERT: G 80 MET cc_start: 0.7408 (mmm) cc_final: 0.6921 (mmm) REVERT: G 130 GLU cc_start: 0.7384 (tp30) cc_final: 0.6770 (pp20) REVERT: G 138 MET cc_start: 0.9114 (tmm) cc_final: 0.8873 (tmm) REVERT: H 70 LYS cc_start: 0.9063 (mtmt) cc_final: 0.8598 (tptt) REVERT: H 74 LEU cc_start: 0.8896 (tp) cc_final: 0.8629 (tp) REVERT: H 165 LYS cc_start: 0.8775 (mmmt) cc_final: 0.8446 (mmmt) REVERT: H 166 ASN cc_start: 0.8285 (m110) cc_final: 0.7333 (t0) REVERT: H 177 ARG cc_start: 0.8988 (tpp-160) cc_final: 0.8516 (tpm170) REVERT: H 203 MET cc_start: 0.8226 (mpp) cc_final: 0.7814 (mpp) REVERT: I 72 MET cc_start: 0.7731 (tpp) cc_final: 0.7421 (mmt) REVERT: I 198 ASN cc_start: 0.7541 (t0) cc_final: 0.6748 (m-40) REVERT: K 8 TYR cc_start: 0.3378 (m-80) cc_final: 0.3025 (m-10) REVERT: K 59 MET cc_start: 0.7563 (tpt) cc_final: 0.7193 (tpt) REVERT: K 84 ASP cc_start: 0.7698 (m-30) cc_final: 0.7462 (m-30) REVERT: K 107 MET cc_start: 0.5796 (mpp) cc_final: 0.5547 (mpp) REVERT: K 156 MET cc_start: 0.7417 (ppp) cc_final: 0.7072 (ppp) REVERT: K 236 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6830 (pm20) REVERT: L 46 LEU cc_start: 0.3633 (OUTLIER) cc_final: 0.3172 (pp) REVERT: L 62 LYS cc_start: 0.7548 (mmmt) cc_final: 0.6696 (mttp) REVERT: M 17 ASP cc_start: 0.8806 (m-30) cc_final: 0.8176 (t70) REVERT: M 66 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6302 (mp) REVERT: U 35 TRP cc_start: 0.8990 (p-90) cc_final: 0.8713 (p-90) REVERT: U 177 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7824 (pp) REVERT: U 188 MET cc_start: 0.7129 (tpt) cc_final: 0.6854 (ppp) REVERT: U 190 ASN cc_start: 0.8760 (m-40) cc_final: 0.8439 (p0) REVERT: U 251 ASP cc_start: 0.8808 (m-30) cc_final: 0.8290 (t0) REVERT: U 556 MET cc_start: 0.8301 (tpt) cc_final: 0.8053 (tpt) REVERT: U 604 HIS cc_start: 0.9243 (OUTLIER) cc_final: 0.7906 (t70) REVERT: U 612 ASP cc_start: 0.8925 (m-30) cc_final: 0.8725 (m-30) REVERT: U 694 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8480 (tt) REVERT: U 738 ASP cc_start: 0.8885 (m-30) cc_final: 0.8650 (m-30) REVERT: U 906 LEU cc_start: 0.8144 (tp) cc_final: 0.7935 (tp) REVERT: V 38 LYS cc_start: 0.9119 (mtmt) cc_final: 0.8842 (mtmm) REVERT: V 139 MET cc_start: 0.9021 (ptm) cc_final: 0.8492 (ppp) REVERT: V 180 ARG cc_start: 0.8722 (mtt180) cc_final: 0.8361 (ptp-170) REVERT: V 301 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7844 (tm-30) REVERT: V 344 ASP cc_start: 0.7467 (t0) cc_final: 0.7096 (t70) REVERT: V 358 MET cc_start: 0.8473 (tmm) cc_final: 0.8136 (tmm) REVERT: V 482 PHE cc_start: 0.8883 (t80) cc_final: 0.8592 (t80) REVERT: V 494 MET cc_start: 0.8649 (mmm) cc_final: 0.8445 (tpt) REVERT: W 123 ARG cc_start: 0.8771 (mmp-170) cc_final: 0.8505 (mmm160) REVERT: W 310 THR cc_start: 0.8816 (m) cc_final: 0.8552 (p) REVERT: X 140 THR cc_start: 0.9534 (OUTLIER) cc_final: 0.9248 (p) REVERT: X 162 ASP cc_start: 0.7888 (t0) cc_final: 0.7458 (t0) REVERT: X 301 ASP cc_start: 0.8706 (t0) cc_final: 0.8427 (t70) REVERT: Y 59 LYS cc_start: 0.9196 (pttt) cc_final: 0.8991 (mmtt) REVERT: Y 73 MET cc_start: 0.7753 (ttm) cc_final: 0.7144 (mmm) REVERT: Y 250 LEU cc_start: 0.9470 (mt) cc_final: 0.9206 (mt) REVERT: Y 293 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7773 (mmt180) REVERT: Z 44 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8357 (mm-40) REVERT: Z 68 TRP cc_start: 0.8832 (p-90) cc_final: 0.8181 (p-90) REVERT: Z 104 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7410 (t0) REVERT: Z 229 GLN cc_start: 0.8264 (tm-30) cc_final: 0.8025 (tm-30) REVERT: a 141 MET cc_start: 0.8506 (ppp) cc_final: 0.8042 (ppp) REVERT: a 142 LEU cc_start: 0.9112 (tp) cc_final: 0.8689 (mt) REVERT: a 278 MET cc_start: 0.9251 (mmm) cc_final: 0.8586 (mpp) REVERT: a 312 MET cc_start: 0.9193 (mtm) cc_final: 0.8816 (mtm) REVERT: b 15 TYR cc_start: 0.9040 (m-80) cc_final: 0.8368 (m-80) REVERT: b 16 MET cc_start: 0.8793 (tpp) cc_final: 0.8547 (tpp) REVERT: b 46 GLU cc_start: 0.9521 (tp30) cc_final: 0.9202 (tp30) REVERT: b 70 ARG cc_start: 0.9148 (tpp80) cc_final: 0.8775 (mmm160) REVERT: b 85 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8930 (p) REVERT: b 107 MET cc_start: 0.7952 (mmp) cc_final: 0.7713 (mmp) REVERT: d 108 ASN cc_start: 0.8585 (t0) cc_final: 0.8355 (t0) REVERT: d 160 ASP cc_start: 0.8607 (t0) cc_final: 0.8302 (t0) REVERT: d 168 MET cc_start: 0.9386 (tpp) cc_final: 0.9130 (tpt) REVERT: d 194 LEU cc_start: 0.9221 (mt) cc_final: 0.8988 (mt) REVERT: d 299 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8587 (mmm) REVERT: d 309 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8118 (p) REVERT: f 58 MET cc_start: 0.9351 (mmm) cc_final: 0.9062 (ppp) REVERT: f 217 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8695 (mp) REVERT: f 275 MET cc_start: 0.8323 (mtm) cc_final: 0.7651 (tmm) REVERT: f 294 MET cc_start: 0.7884 (ptp) cc_final: 0.7004 (ptt) REVERT: f 297 MET cc_start: 0.9084 (mtt) cc_final: 0.8761 (mtt) REVERT: f 305 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7639 (pp) REVERT: f 309 GLU cc_start: 0.8319 (tp30) cc_final: 0.7608 (pm20) REVERT: f 313 GLU cc_start: 0.7609 (mp0) cc_final: 0.7283 (mp0) REVERT: f 340 MET cc_start: 0.7472 (mmm) cc_final: 0.7146 (mmm) REVERT: f 416 MET cc_start: 0.9050 (mtm) cc_final: 0.8716 (mtm) REVERT: f 485 LEU cc_start: 0.8854 (tp) cc_final: 0.8609 (pp) REVERT: f 543 MET cc_start: 0.7046 (tpp) cc_final: 0.6779 (mmm) REVERT: f 744 MET cc_start: 0.9449 (mtt) cc_final: 0.9162 (mtt) REVERT: f 784 ASP cc_start: 0.8453 (t0) cc_final: 0.8150 (t70) REVERT: f 885 GLU cc_start: 0.9358 (pm20) cc_final: 0.9000 (mp0) REVERT: g 95 LYS cc_start: 0.4111 (tppt) cc_final: 0.3655 (tttt) REVERT: g 159 LYS cc_start: 0.4645 (mmtm) cc_final: 0.4407 (mmmt) REVERT: u 178 TYR cc_start: 0.8828 (t80) cc_final: 0.8101 (t80) REVERT: u 266 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8707 (tp) REVERT: u 285 LYS cc_start: 0.7832 (mttt) cc_final: 0.7344 (mmmt) outliers start: 307 outliers final: 212 residues processed: 1056 average time/residue: 0.6893 time to fit residues: 1254.7616 Evaluate side-chains 1012 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 776 time to evaluate : 6.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 420 TYR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 351 LYS Chi-restraints excluded: chain G residue 23 TYR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 163 HIS Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 14 PHE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 165 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 244 MET Chi-restraints excluded: chain U residue 249 CYS Chi-restraints excluded: chain U residue 252 LEU Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 366 HIS Chi-restraints excluded: chain U residue 367 THR Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 411 ILE Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 552 ILE Chi-restraints excluded: chain U residue 593 SER Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 604 HIS Chi-restraints excluded: chain U residue 685 GLN Chi-restraints excluded: chain U residue 694 ILE Chi-restraints excluded: chain U residue 706 VAL Chi-restraints excluded: chain U residue 711 GLN Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 835 ILE Chi-restraints excluded: chain U residue 875 PHE Chi-restraints excluded: chain U residue 921 ILE Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 135 LEU Chi-restraints excluded: chain V residue 144 ASP Chi-restraints excluded: chain V residue 147 PHE Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 174 PHE Chi-restraints excluded: chain V residue 175 MET Chi-restraints excluded: chain V residue 194 LYS Chi-restraints excluded: chain V residue 212 TYR Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 230 PHE Chi-restraints excluded: chain V residue 249 THR Chi-restraints excluded: chain V residue 263 LEU Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 346 LEU Chi-restraints excluded: chain V residue 392 TYR Chi-restraints excluded: chain V residue 394 LEU Chi-restraints excluded: chain V residue 422 ILE Chi-restraints excluded: chain V residue 443 ARG Chi-restraints excluded: chain W residue 60 MET Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 115 ILE Chi-restraints excluded: chain W residue 376 LYS Chi-restraints excluded: chain W residue 427 ASP Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 177 TYR Chi-restraints excluded: chain X residue 256 LEU Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 388 PHE Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 416 ASN Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 136 HIS Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Y residue 180 LEU Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 220 VAL Chi-restraints excluded: chain Y residue 288 PHE Chi-restraints excluded: chain Y residue 293 ARG Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 72 HIS Chi-restraints excluded: chain Z residue 104 ASN Chi-restraints excluded: chain Z residue 135 THR Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 182 THR Chi-restraints excluded: chain Z residue 227 ILE Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 231 GLN Chi-restraints excluded: chain Z residue 266 ILE Chi-restraints excluded: chain Z residue 278 ASN Chi-restraints excluded: chain a residue 60 TYR Chi-restraints excluded: chain a residue 118 ILE Chi-restraints excluded: chain a residue 138 VAL Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 275 LEU Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 296 ILE Chi-restraints excluded: chain a residue 310 LEU Chi-restraints excluded: chain a residue 343 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 84 ILE Chi-restraints excluded: chain b residue 85 THR Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 118 PHE Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 181 LEU Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 218 LEU Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 223 ASN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 242 ASN Chi-restraints excluded: chain d residue 245 PHE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain e residue 65 TYR Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 125 ILE Chi-restraints excluded: chain f residue 177 GLU Chi-restraints excluded: chain f residue 217 LEU Chi-restraints excluded: chain f residue 231 LEU Chi-restraints excluded: chain f residue 256 PHE Chi-restraints excluded: chain f residue 266 LEU Chi-restraints excluded: chain f residue 305 LEU Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 365 VAL Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 510 SER Chi-restraints excluded: chain f residue 573 ILE Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 747 GLN Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 810 ILE Chi-restraints excluded: chain f residue 832 THR Chi-restraints excluded: chain f residue 852 VAL Chi-restraints excluded: chain f residue 898 VAL Chi-restraints excluded: chain f residue 905 ASN Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 167 ILE Chi-restraints excluded: chain u residue 182 PHE Chi-restraints excluded: chain u residue 241 VAL Chi-restraints excluded: chain u residue 244 VAL Chi-restraints excluded: chain u residue 266 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 163 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 615 optimal weight: 0.9990 chunk 864 optimal weight: 10.0000 chunk 740 optimal weight: 10.0000 chunk 332 optimal weight: 6.9990 chunk 339 optimal weight: 5.9990 chunk 643 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 487 optimal weight: 8.9990 chunk 698 optimal weight: 0.0170 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN ** I 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 GLN L 20 HIS U 190 ASN ** U 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 262 ASN ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 160 GLN ** u 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.075528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.057993 restraints weight = 290607.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.059238 restraints weight = 176913.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.060061 restraints weight = 127349.652| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.7144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 71563 Z= 0.212 Angle : 0.756 17.806 96729 Z= 0.374 Chirality : 0.044 0.318 11063 Planarity : 0.004 0.075 12470 Dihedral : 7.073 163.312 9847 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.87 % Favored : 93.72 % Rotamer: Outliers : 3.28 % Allowed : 23.00 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -0.13 (0.09), residues: 8837 helix: 0.72 (0.08), residues: 4804 sheet: -0.70 (0.17), residues: 928 loop : -1.04 (0.12), residues: 3105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP a 255 HIS 0.014 0.001 HIS U 754 PHE 0.039 0.002 PHE c 160 TYR 0.025 0.002 TYR W 75 ARG 0.011 0.001 ARG B 363 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 876 time to evaluate : 6.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.9168 (mmm) cc_final: 0.8924 (mmm) REVERT: A 420 TYR cc_start: 0.4396 (OUTLIER) cc_final: 0.3662 (m-80) REVERT: B 75 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8697 (mm-30) REVERT: B 92 GLN cc_start: 0.8296 (mt0) cc_final: 0.8039 (pm20) REVERT: B 114 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8019 (mt-10) REVERT: B 177 GLU cc_start: 0.8138 (tp30) cc_final: 0.7572 (tt0) REVERT: B 183 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8308 (p) REVERT: B 363 ARG cc_start: 0.9027 (mmm160) cc_final: 0.8644 (tpp80) REVERT: B 404 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9308 (mm) REVERT: B 405 MET cc_start: 0.9021 (mtp) cc_final: 0.8702 (mtp) REVERT: C 62 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8713 (tm-30) REVERT: C 150 MET cc_start: 0.8905 (ptp) cc_final: 0.8570 (pmm) REVERT: C 385 MET cc_start: 0.8844 (ptt) cc_final: 0.8465 (ptm) REVERT: C 391 MET cc_start: 0.8629 (ptm) cc_final: 0.7906 (ptm) REVERT: C 396 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8617 (mm-30) REVERT: C 399 MET cc_start: 0.7871 (mmp) cc_final: 0.7478 (mmp) REVERT: C 403 LYS cc_start: 0.5804 (OUTLIER) cc_final: 0.5273 (ptpp) REVERT: D 60 TYR cc_start: 0.9159 (OUTLIER) cc_final: 0.8299 (t80) REVERT: D 71 GLU cc_start: 0.8696 (tp30) cc_final: 0.8429 (tp30) REVERT: D 83 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8677 (pm20) REVERT: D 97 ASP cc_start: 0.9042 (t0) cc_final: 0.8742 (t70) REVERT: D 98 GLN cc_start: 0.8819 (mp10) cc_final: 0.8589 (mp10) REVERT: D 170 MET cc_start: 0.8559 (mtm) cc_final: 0.8322 (pmm) REVERT: D 287 ARG cc_start: 0.9122 (mtm-85) cc_final: 0.8886 (mtm-85) REVERT: D 356 GLU cc_start: 0.9257 (tp30) cc_final: 0.8825 (pm20) REVERT: E 258 MET cc_start: 0.8356 (tmm) cc_final: 0.8136 (tmm) REVERT: E 275 MET cc_start: 0.9231 (mmm) cc_final: 0.8991 (mmm) REVERT: F 53 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6642 (pttt) REVERT: F 71 ASP cc_start: 0.8569 (m-30) cc_final: 0.8329 (m-30) REVERT: F 288 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9453 (mm) REVERT: F 310 MET cc_start: 0.9189 (ppp) cc_final: 0.8735 (ppp) REVERT: F 316 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8684 (mm110) REVERT: F 351 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.8578 (mtmt) REVERT: F 421 MET cc_start: 0.9078 (mmm) cc_final: 0.8699 (mmm) REVERT: F 437 TYR cc_start: 0.7367 (m-10) cc_final: 0.6677 (m-10) REVERT: G 80 MET cc_start: 0.7336 (mmm) cc_final: 0.6933 (mmm) REVERT: H 70 LYS cc_start: 0.9017 (mtmt) cc_final: 0.8503 (tptt) REVERT: H 74 LEU cc_start: 0.8798 (tp) cc_final: 0.8414 (tp) REVERT: H 165 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8542 (mmmt) REVERT: H 166 ASN cc_start: 0.8252 (m110) cc_final: 0.7454 (t0) REVERT: H 177 ARG cc_start: 0.8921 (tpp-160) cc_final: 0.8514 (tpm170) REVERT: H 203 MET cc_start: 0.8195 (mpp) cc_final: 0.7785 (mpp) REVERT: I 198 ASN cc_start: 0.7434 (t0) cc_final: 0.6715 (m-40) REVERT: J 15 HIS cc_start: 0.8367 (m90) cc_final: 0.8078 (m90) REVERT: K 8 TYR cc_start: 0.2993 (m-80) cc_final: 0.2715 (m-10) REVERT: K 59 MET cc_start: 0.7635 (tpt) cc_final: 0.7014 (tpt) REVERT: K 84 ASP cc_start: 0.7773 (m-30) cc_final: 0.7557 (m-30) REVERT: K 156 MET cc_start: 0.7219 (ppp) cc_final: 0.6965 (ppp) REVERT: K 206 MET cc_start: 0.7229 (mmp) cc_final: 0.6985 (mmt) REVERT: L 46 LEU cc_start: 0.4330 (OUTLIER) cc_final: 0.3780 (pp) REVERT: L 62 LYS cc_start: 0.7585 (mmmt) cc_final: 0.6844 (mttp) REVERT: M 17 ASP cc_start: 0.8574 (m-30) cc_final: 0.7999 (t70) REVERT: M 66 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6314 (mp) REVERT: U 35 TRP cc_start: 0.9014 (p-90) cc_final: 0.8665 (p-90) REVERT: U 177 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7892 (pp) REVERT: U 188 MET cc_start: 0.7060 (tpt) cc_final: 0.6644 (ppp) REVERT: U 520 MET cc_start: 0.8784 (mmm) cc_final: 0.8121 (mmm) REVERT: U 556 MET cc_start: 0.8415 (tpt) cc_final: 0.8182 (tpt) REVERT: U 604 HIS cc_start: 0.9227 (OUTLIER) cc_final: 0.8093 (t70) REVERT: U 612 ASP cc_start: 0.9041 (m-30) cc_final: 0.8794 (m-30) REVERT: U 694 ILE cc_start: 0.8672 (tt) cc_final: 0.8414 (tt) REVERT: U 738 ASP cc_start: 0.8806 (m-30) cc_final: 0.8088 (t0) REVERT: U 757 MET cc_start: 0.8656 (tmm) cc_final: 0.8420 (tmm) REVERT: U 906 LEU cc_start: 0.8221 (tp) cc_final: 0.7757 (tp) REVERT: V 38 LYS cc_start: 0.9101 (mtmt) cc_final: 0.8809 (mtmm) REVERT: V 139 MET cc_start: 0.9081 (ptm) cc_final: 0.8403 (ppp) REVERT: V 299 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8430 (tm-30) REVERT: V 301 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7803 (tm-30) REVERT: V 344 ASP cc_start: 0.7586 (t0) cc_final: 0.7234 (t70) REVERT: V 358 MET cc_start: 0.8434 (tmm) cc_final: 0.8095 (tmm) REVERT: V 482 PHE cc_start: 0.8825 (t80) cc_final: 0.8518 (t80) REVERT: W 104 MET cc_start: 0.8254 (ptm) cc_final: 0.8027 (ptm) REVERT: X 140 THR cc_start: 0.9532 (OUTLIER) cc_final: 0.9306 (p) REVERT: X 162 ASP cc_start: 0.7824 (t0) cc_final: 0.7597 (t0) REVERT: X 270 LEU cc_start: 0.9522 (mm) cc_final: 0.9230 (mm) REVERT: Y 59 LYS cc_start: 0.9204 (pttt) cc_final: 0.8920 (mmtt) REVERT: Y 105 MET cc_start: 0.7978 (mmm) cc_final: 0.7733 (mmm) REVERT: Y 250 LEU cc_start: 0.9403 (mt) cc_final: 0.9133 (mt) REVERT: Y 293 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7754 (mmt180) REVERT: Z 44 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8294 (mm-40) REVERT: Z 261 TYR cc_start: 0.9213 (t80) cc_final: 0.8974 (t80) REVERT: a 141 MET cc_start: 0.8610 (ppp) cc_final: 0.8204 (ppp) REVERT: a 142 LEU cc_start: 0.9184 (tp) cc_final: 0.8705 (mt) REVERT: a 180 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8966 (tt) REVERT: a 278 MET cc_start: 0.9168 (mmm) cc_final: 0.8457 (mpp) REVERT: a 312 MET cc_start: 0.9063 (mtm) cc_final: 0.8709 (mtm) REVERT: a 335 TRP cc_start: 0.7578 (t-100) cc_final: 0.6833 (t60) REVERT: a 360 VAL cc_start: 0.9617 (t) cc_final: 0.9383 (t) REVERT: a 365 MET cc_start: 0.8813 (ptp) cc_final: 0.8603 (ptt) REVERT: b 15 TYR cc_start: 0.9080 (m-80) cc_final: 0.8474 (m-80) REVERT: b 16 MET cc_start: 0.8841 (tpp) cc_final: 0.8457 (tpp) REVERT: b 54 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8702 (mp) REVERT: b 107 MET cc_start: 0.7952 (mmp) cc_final: 0.7436 (mmt) REVERT: c 289 ASP cc_start: 0.8847 (t0) cc_final: 0.8625 (t0) REVERT: d 160 ASP cc_start: 0.8488 (t0) cc_final: 0.8181 (t0) REVERT: d 194 LEU cc_start: 0.9123 (mt) cc_final: 0.8903 (mt) REVERT: d 211 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8858 (mm-30) REVERT: d 237 MET cc_start: 0.8650 (mmm) cc_final: 0.8345 (mmm) REVERT: d 309 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8043 (p) REVERT: d 327 ASP cc_start: 0.7592 (t70) cc_final: 0.7159 (t70) REVERT: e 62 LYS cc_start: 0.8705 (pttt) cc_final: 0.8338 (pttm) REVERT: e 63 HIS cc_start: 0.7693 (m170) cc_final: 0.7107 (m170) REVERT: f 58 MET cc_start: 0.9368 (mmm) cc_final: 0.9055 (ppp) REVERT: f 217 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8634 (mp) REVERT: f 275 MET cc_start: 0.8346 (mtm) cc_final: 0.7719 (tmm) REVERT: f 294 MET cc_start: 0.7831 (ptp) cc_final: 0.6987 (ptt) REVERT: f 297 MET cc_start: 0.9066 (mtt) cc_final: 0.8738 (mtt) REVERT: f 305 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7927 (pp) REVERT: f 309 GLU cc_start: 0.8369 (tp30) cc_final: 0.7521 (pm20) REVERT: f 340 MET cc_start: 0.7627 (mmm) cc_final: 0.7380 (mmm) REVERT: f 416 MET cc_start: 0.9013 (mtm) cc_final: 0.8743 (mtm) REVERT: f 477 MET cc_start: 0.8499 (mmm) cc_final: 0.6770 (tpt) REVERT: f 485 LEU cc_start: 0.8805 (tp) cc_final: 0.8496 (pp) REVERT: f 744 MET cc_start: 0.9473 (mtt) cc_final: 0.9092 (mtt) REVERT: f 784 ASP cc_start: 0.8332 (t0) cc_final: 0.8128 (t70) REVERT: g 94 LYS cc_start: 0.6965 (mmtp) cc_final: 0.6704 (mmtm) REVERT: g 95 LYS cc_start: 0.4167 (tppt) cc_final: 0.3695 (tttt) REVERT: u 151 ARG cc_start: 0.8777 (mmm160) cc_final: 0.8524 (mmm160) REVERT: u 178 TYR cc_start: 0.8754 (t80) cc_final: 0.7981 (t80) REVERT: u 266 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8743 (tp) REVERT: u 285 LYS cc_start: 0.7742 (mttt) cc_final: 0.7225 (mmmt) outliers start: 250 outliers final: 184 residues processed: 1055 average time/residue: 0.6911 time to fit residues: 1252.8802 Evaluate side-chains 1001 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 795 time to evaluate : 6.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 420 TYR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 351 LYS Chi-restraints excluded: chain G residue 23 TYR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 163 HIS Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain L residue 123 TYR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 14 PHE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 165 ILE Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain U residue 168 LEU Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 249 CYS Chi-restraints excluded: chain U residue 252 LEU Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 366 HIS Chi-restraints excluded: chain U residue 367 THR Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 604 HIS Chi-restraints excluded: chain U residue 685 GLN Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 835 ILE Chi-restraints excluded: chain U residue 921 ILE Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 135 LEU Chi-restraints excluded: chain V residue 144 ASP Chi-restraints excluded: chain V residue 147 PHE Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 175 MET Chi-restraints excluded: chain V residue 194 LYS Chi-restraints excluded: chain V residue 212 TYR Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 230 PHE Chi-restraints excluded: chain V residue 263 LEU Chi-restraints excluded: chain V residue 303 SER Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 338 LEU Chi-restraints excluded: chain V residue 346 LEU Chi-restraints excluded: chain V residue 394 LEU Chi-restraints excluded: chain V residue 422 ILE Chi-restraints excluded: chain V residue 443 ARG Chi-restraints excluded: chain W residue 60 MET Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 216 GLU Chi-restraints excluded: chain W residue 427 ASP Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 256 LEU Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 388 PHE Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 416 ASN Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 136 HIS Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Y residue 180 LEU Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 220 VAL Chi-restraints excluded: chain Y residue 293 ARG Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 182 THR Chi-restraints excluded: chain Z residue 195 VAL Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 231 GLN Chi-restraints excluded: chain Z residue 266 ILE Chi-restraints excluded: chain Z residue 278 ASN Chi-restraints excluded: chain a residue 60 TYR Chi-restraints excluded: chain a residue 180 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 275 LEU Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 310 LEU Chi-restraints excluded: chain a residue 343 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 84 ILE Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 118 PHE Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 218 LEU Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 242 ASN Chi-restraints excluded: chain d residue 245 PHE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 217 LEU Chi-restraints excluded: chain f residue 231 LEU Chi-restraints excluded: chain f residue 256 PHE Chi-restraints excluded: chain f residue 266 LEU Chi-restraints excluded: chain f residue 305 LEU Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 487 LEU Chi-restraints excluded: chain f residue 510 SER Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 852 VAL Chi-restraints excluded: chain f residue 898 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 167 ILE Chi-restraints excluded: chain u residue 182 PHE Chi-restraints excluded: chain u residue 244 VAL Chi-restraints excluded: chain u residue 266 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 114 optimal weight: 0.0170 chunk 275 optimal weight: 40.0000 chunk 755 optimal weight: 7.9990 chunk 613 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 208 optimal weight: 0.3980 chunk 668 optimal weight: 6.9990 chunk 520 optimal weight: 9.9990 chunk 632 optimal weight: 8.9990 chunk 683 optimal weight: 6.9990 chunk 475 optimal weight: 0.0670 overall best weight: 1.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS A 293 ASN B 81 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN E 300 HIS ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN ** U 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 260 HIS ** X 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 7 GLN Z 223 ASN ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 108 ASN ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.085794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.068758 restraints weight = 368692.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.070875 restraints weight = 212243.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.071949 restraints weight = 128250.375| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.7293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 71563 Z= 0.206 Angle : 0.769 17.999 96729 Z= 0.378 Chirality : 0.045 0.308 11063 Planarity : 0.004 0.073 12470 Dihedral : 6.891 159.467 9842 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.26 % Favored : 93.37 % Rotamer: Outliers : 3.05 % Allowed : 23.58 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.01 % 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: -0.09 (0.09), residues: 8837 helix: 0.75 (0.08), residues: 4816 sheet: -0.75 (0.16), residues: 948 loop : -0.99 (0.12), residues: 3073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP a 255 HIS 0.014 0.001 HIS U 754 PHE 0.026 0.002 PHE E 338 TYR 0.024 0.001 TYR u 262 ARG 0.020 0.001 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 856 time to evaluate : 6.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8994 (mmtm) cc_final: 0.8443 (ptmt) REVERT: A 118 PHE cc_start: 0.8506 (t80) cc_final: 0.8275 (t80) REVERT: A 164 MET cc_start: 0.9280 (ttm) cc_final: 0.8839 (ttm) REVERT: A 293 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8262 (t0) REVERT: A 332 MET cc_start: 0.9202 (mmm) cc_final: 0.8946 (mmm) REVERT: A 420 TYR cc_start: 0.4471 (OUTLIER) cc_final: 0.3789 (m-80) REVERT: B 69 LYS cc_start: 0.9345 (tttp) cc_final: 0.9077 (mmmt) REVERT: B 75 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8475 (mm-30) REVERT: B 92 GLN cc_start: 0.8381 (mt0) cc_final: 0.8127 (pm20) REVERT: B 114 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8571 (mt-10) REVERT: B 183 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8271 (p) REVERT: B 225 TYR cc_start: 0.8254 (p90) cc_final: 0.8053 (p90) REVERT: B 404 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9303 (mm) REVERT: B 405 MET cc_start: 0.9056 (mtp) cc_final: 0.8692 (mtp) REVERT: C 62 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8689 (tm-30) REVERT: C 81 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.7170 (p0) REVERT: C 385 MET cc_start: 0.8782 (ptt) cc_final: 0.8379 (ptm) REVERT: C 396 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8546 (mm-30) REVERT: C 399 MET cc_start: 0.7772 (mmp) cc_final: 0.7306 (mmt) REVERT: C 403 LYS cc_start: 0.5716 (OUTLIER) cc_final: 0.5210 (ptpp) REVERT: D 60 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8228 (t80) REVERT: D 71 GLU cc_start: 0.8721 (tp30) cc_final: 0.8439 (tp30) REVERT: D 97 ASP cc_start: 0.9062 (t0) cc_final: 0.8713 (t70) REVERT: D 98 GLN cc_start: 0.8935 (mp10) cc_final: 0.8691 (mp10) REVERT: D 287 ARG cc_start: 0.9152 (mtm-85) cc_final: 0.8911 (mtm-85) REVERT: D 356 GLU cc_start: 0.9261 (tp30) cc_final: 0.8767 (pm20) REVERT: E 258 MET cc_start: 0.8342 (tmm) cc_final: 0.8066 (tmm) REVERT: F 53 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6814 (pttt) REVERT: F 71 ASP cc_start: 0.8581 (m-30) cc_final: 0.8318 (m-30) REVERT: F 310 MET cc_start: 0.9040 (ppp) cc_final: 0.8566 (ppp) REVERT: F 316 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8597 (mm110) REVERT: F 351 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8899 (mtmm) REVERT: F 421 MET cc_start: 0.8959 (mmm) cc_final: 0.8604 (mmm) REVERT: F 437 TYR cc_start: 0.7122 (m-10) cc_final: 0.6549 (m-10) REVERT: G 80 MET cc_start: 0.7318 (mmm) cc_final: 0.6307 (mmm) REVERT: H 70 LYS cc_start: 0.9009 (mtmt) cc_final: 0.8580 (tptt) REVERT: H 74 LEU cc_start: 0.8876 (tp) cc_final: 0.8517 (tp) REVERT: H 119 GLN cc_start: 0.9522 (tm-30) cc_final: 0.9217 (tp-100) REVERT: H 165 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8519 (mmmt) REVERT: H 166 ASN cc_start: 0.8251 (m110) cc_final: 0.7414 (t0) REVERT: H 173 PHE cc_start: 0.8622 (t80) cc_final: 0.8071 (t80) REVERT: H 177 ARG cc_start: 0.8976 (tpp-160) cc_final: 0.8500 (tpm170) REVERT: H 203 MET cc_start: 0.8106 (mpp) cc_final: 0.7698 (mpp) REVERT: I 25 MET cc_start: 0.9050 (mtt) cc_final: 0.8797 (mpp) REVERT: I 198 ASN cc_start: 0.7467 (t0) cc_final: 0.6722 (m-40) REVERT: J 15 HIS cc_start: 0.8111 (m90) cc_final: 0.7834 (m90) REVERT: J 114 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8996 (pp) REVERT: K 8 TYR cc_start: 0.3011 (m-80) cc_final: 0.2730 (m-10) REVERT: K 59 MET cc_start: 0.7413 (tpt) cc_final: 0.6746 (tpt) REVERT: K 107 MET cc_start: 0.5632 (mpp) cc_final: 0.5327 (mpp) REVERT: K 156 MET cc_start: 0.7291 (ppp) cc_final: 0.7036 (ppp) REVERT: L 26 MET cc_start: 0.8515 (mmm) cc_final: 0.8247 (mmm) REVERT: L 46 LEU cc_start: 0.3814 (OUTLIER) cc_final: 0.3272 (pp) REVERT: L 62 LYS cc_start: 0.7484 (mmmt) cc_final: 0.6616 (mttp) REVERT: L 64 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7214 (mm) REVERT: L 159 MET cc_start: 0.2200 (ttp) cc_final: 0.1911 (ptm) REVERT: M 17 ASP cc_start: 0.8786 (m-30) cc_final: 0.8125 (t70) REVERT: M 66 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6367 (mp) REVERT: M 180 GLN cc_start: 0.7686 (tp-100) cc_final: 0.7433 (tm-30) REVERT: M 184 MET cc_start: 0.6731 (ptm) cc_final: 0.6019 (ppp) REVERT: U 35 TRP cc_start: 0.8957 (p-90) cc_final: 0.8697 (p-90) REVERT: U 188 MET cc_start: 0.7008 (tpt) cc_final: 0.6627 (ppp) REVERT: U 520 MET cc_start: 0.8784 (mmm) cc_final: 0.8237 (mmm) REVERT: U 604 HIS cc_start: 0.9208 (OUTLIER) cc_final: 0.8043 (t70) REVERT: U 612 ASP cc_start: 0.8864 (m-30) cc_final: 0.8658 (m-30) REVERT: U 694 ILE cc_start: 0.8600 (tt) cc_final: 0.8395 (tt) REVERT: U 727 LYS cc_start: 0.9020 (ptpt) cc_final: 0.8717 (ptpp) REVERT: V 38 LYS cc_start: 0.9044 (mtmt) cc_final: 0.8716 (ptpp) REVERT: V 139 MET cc_start: 0.9024 (ptm) cc_final: 0.8315 (ppp) REVERT: V 299 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8310 (tm-30) REVERT: V 301 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7830 (tm-30) REVERT: V 344 ASP cc_start: 0.7593 (t0) cc_final: 0.7223 (t70) REVERT: V 358 MET cc_start: 0.8385 (tmm) cc_final: 0.8035 (tmm) REVERT: V 482 PHE cc_start: 0.8902 (t80) cc_final: 0.8555 (t80) REVERT: V 494 MET cc_start: 0.8178 (tpt) cc_final: 0.7808 (tpp) REVERT: W 104 MET cc_start: 0.8531 (ptm) cc_final: 0.8203 (ptm) REVERT: W 198 ASP cc_start: 0.7947 (t0) cc_final: 0.7592 (m-30) REVERT: X 99 MET cc_start: 0.8062 (ptm) cc_final: 0.7844 (ptt) REVERT: X 140 THR cc_start: 0.9539 (OUTLIER) cc_final: 0.9303 (p) REVERT: X 161 ASP cc_start: 0.7435 (m-30) cc_final: 0.6849 (t70) REVERT: X 162 ASP cc_start: 0.7943 (t0) cc_final: 0.7549 (t0) REVERT: X 270 LEU cc_start: 0.9501 (mm) cc_final: 0.9224 (mm) REVERT: X 304 LYS cc_start: 0.9310 (ptpt) cc_final: 0.8863 (tppt) REVERT: Y 59 LYS cc_start: 0.9154 (pttt) cc_final: 0.8894 (mmtt) REVERT: Y 73 MET cc_start: 0.7634 (ttm) cc_final: 0.7165 (mmm) REVERT: Y 250 LEU cc_start: 0.9438 (mt) cc_final: 0.9150 (mt) REVERT: Z 44 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8317 (mm-40) REVERT: a 109 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6325 (tp30) REVERT: a 141 MET cc_start: 0.8447 (ppp) cc_final: 0.7992 (ppp) REVERT: a 142 LEU cc_start: 0.9046 (tp) cc_final: 0.8674 (mt) REVERT: a 278 MET cc_start: 0.8996 (mmm) cc_final: 0.8702 (mpp) REVERT: a 312 MET cc_start: 0.9098 (mtm) cc_final: 0.8740 (mtm) REVERT: a 335 TRP cc_start: 0.6471 (t60) cc_final: 0.6085 (t-100) REVERT: a 360 VAL cc_start: 0.9627 (t) cc_final: 0.9398 (t) REVERT: a 365 MET cc_start: 0.8824 (ptp) cc_final: 0.8610 (ptt) REVERT: b 15 TYR cc_start: 0.9061 (m-80) cc_final: 0.8491 (m-80) REVERT: b 16 MET cc_start: 0.8882 (tpp) cc_final: 0.8567 (tpp) REVERT: b 70 ARG cc_start: 0.9165 (tpp80) cc_final: 0.8577 (mmm160) REVERT: b 107 MET cc_start: 0.7758 (mmp) cc_final: 0.7372 (mmt) REVERT: c 289 ASP cc_start: 0.8888 (t0) cc_final: 0.8669 (t0) REVERT: d 160 ASP cc_start: 0.8667 (t0) cc_final: 0.8281 (t0) REVERT: d 194 LEU cc_start: 0.9211 (mt) cc_final: 0.8994 (mt) REVERT: d 237 MET cc_start: 0.8650 (mmm) cc_final: 0.8372 (mmm) REVERT: d 309 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8070 (p) REVERT: d 327 ASP cc_start: 0.7339 (t70) cc_final: 0.6936 (t70) REVERT: e 62 LYS cc_start: 0.8680 (pttt) cc_final: 0.8356 (pttm) REVERT: f 52 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9016 (tt) REVERT: f 58 MET cc_start: 0.9398 (mmm) cc_final: 0.9064 (ppp) REVERT: f 275 MET cc_start: 0.8348 (mtm) cc_final: 0.7767 (tmm) REVERT: f 294 MET cc_start: 0.7774 (ptp) cc_final: 0.6968 (ptt) REVERT: f 297 MET cc_start: 0.9090 (mtt) cc_final: 0.8756 (mtt) REVERT: f 305 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8082 (pp) REVERT: f 309 GLU cc_start: 0.8452 (tp30) cc_final: 0.7528 (pm20) REVERT: f 416 MET cc_start: 0.9020 (mtm) cc_final: 0.8730 (mtm) REVERT: f 477 MET cc_start: 0.8566 (mmm) cc_final: 0.6835 (tpt) REVERT: f 485 LEU cc_start: 0.8824 (tp) cc_final: 0.8596 (pp) REVERT: f 524 MET cc_start: 0.8683 (ptt) cc_final: 0.8423 (ptt) REVERT: f 670 MET cc_start: 0.8910 (mmp) cc_final: 0.8700 (mmm) REVERT: f 744 MET cc_start: 0.9359 (mtt) cc_final: 0.9108 (mtt) REVERT: f 800 LEU cc_start: 0.9693 (mp) cc_final: 0.9420 (mp) REVERT: f 829 MET cc_start: 0.7340 (pmm) cc_final: 0.7114 (pmm) REVERT: g 94 LYS cc_start: 0.6958 (mmtp) cc_final: 0.6719 (mmtm) REVERT: g 95 LYS cc_start: 0.4237 (tppt) cc_final: 0.3814 (tttt) REVERT: g 113 ARG cc_start: 0.8353 (ttp-170) cc_final: 0.8082 (ttp-110) REVERT: u 178 TYR cc_start: 0.8741 (t80) cc_final: 0.7972 (t80) REVERT: u 266 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8762 (tp) REVERT: u 285 LYS cc_start: 0.7818 (mttt) cc_final: 0.7276 (mmmt) outliers start: 232 outliers final: 174 residues processed: 1023 average time/residue: 0.6547 time to fit residues: 1149.2961 Evaluate side-chains 1003 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 808 time to evaluate : 6.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 420 TYR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 351 LYS Chi-restraints excluded: chain G residue 23 TYR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 123 GLN Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 163 HIS Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 14 PHE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain U residue 185 MET Chi-restraints excluded: chain U residue 244 MET Chi-restraints excluded: chain U residue 252 LEU Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 366 HIS Chi-restraints excluded: chain U residue 367 THR Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 604 HIS Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 835 ILE Chi-restraints excluded: chain U residue 921 ILE Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 135 LEU Chi-restraints excluded: chain V residue 147 PHE Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 194 LYS Chi-restraints excluded: chain V residue 212 TYR Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 230 PHE Chi-restraints excluded: chain V residue 263 LEU Chi-restraints excluded: chain V residue 303 SER Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 346 LEU Chi-restraints excluded: chain V residue 394 LEU Chi-restraints excluded: chain V residue 422 ILE Chi-restraints excluded: chain V residue 443 ARG Chi-restraints excluded: chain W residue 60 MET Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 216 GLU Chi-restraints excluded: chain W residue 351 TRP Chi-restraints excluded: chain W residue 427 ASP Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 256 LEU Chi-restraints excluded: chain X residue 388 PHE Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 416 ASN Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 136 HIS Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 220 VAL Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 92 VAL Chi-restraints excluded: chain Z residue 135 THR Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 182 THR Chi-restraints excluded: chain Z residue 227 ILE Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 231 GLN Chi-restraints excluded: chain Z residue 278 ASN Chi-restraints excluded: chain a residue 60 TYR Chi-restraints excluded: chain a residue 109 GLU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 275 LEU Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 310 LEU Chi-restraints excluded: chain a residue 343 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 118 PHE Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 179 SER Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 218 LEU Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain d residue 108 ASN Chi-restraints excluded: chain d residue 242 ASN Chi-restraints excluded: chain d residue 245 PHE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 52 LEU Chi-restraints excluded: chain f residue 177 GLU Chi-restraints excluded: chain f residue 231 LEU Chi-restraints excluded: chain f residue 256 PHE Chi-restraints excluded: chain f residue 305 LEU Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 487 LEU Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 852 VAL Chi-restraints excluded: chain f residue 898 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 167 ILE Chi-restraints excluded: chain u residue 182 PHE Chi-restraints excluded: chain u residue 244 VAL Chi-restraints excluded: chain u residue 266 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 811 optimal weight: 5.9990 chunk 575 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 873 optimal weight: 0.0970 chunk 405 optimal weight: 9.9990 chunk 416 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 665 optimal weight: 0.3980 chunk 794 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 206 optimal weight: 0.9980 overall best weight: 2.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN L 20 HIS ** U 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 440 ASN ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 278 ASN ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 108 ASN ** d 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN ** f 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.086231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.069529 restraints weight = 365711.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.071062 restraints weight = 201184.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.072034 restraints weight = 133595.284| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.7446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 71563 Z= 0.233 Angle : 0.779 15.221 96729 Z= 0.383 Chirality : 0.045 0.308 11063 Planarity : 0.004 0.073 12470 Dihedral : 6.876 161.028 9842 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.26 % Favored : 93.37 % Rotamer: Outliers : 2.85 % Allowed : 24.00 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.01 % 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: -0.08 (0.09), residues: 8837 helix: 0.75 (0.08), residues: 4838 sheet: -0.75 (0.17), residues: 926 loop : -1.02 (0.12), residues: 3073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP a 335 HIS 0.015 0.001 HIS U 754 PHE 0.032 0.002 PHE E 338 TYR 0.029 0.002 TYR H 121 ARG 0.016 0.001 ARG C 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17674 Ramachandran restraints generated. 8837 Oldfield, 0 Emsley, 8837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 814 time to evaluate : 6.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 PHE cc_start: 0.8497 (t80) cc_final: 0.8273 (t80) REVERT: A 164 MET cc_start: 0.9314 (ttm) cc_final: 0.8912 (ttm) REVERT: A 293 ASN cc_start: 0.8726 (t0) cc_final: 0.8081 (t0) REVERT: A 332 MET cc_start: 0.9236 (mmm) cc_final: 0.8982 (mmm) REVERT: A 420 TYR cc_start: 0.4483 (OUTLIER) cc_final: 0.3837 (m-80) REVERT: B 69 LYS cc_start: 0.9380 (tttp) cc_final: 0.9076 (mmmt) REVERT: B 75 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8807 (mm-30) REVERT: B 92 GLN cc_start: 0.8269 (mt0) cc_final: 0.8038 (pm20) REVERT: B 114 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8526 (mt-10) REVERT: B 177 GLU cc_start: 0.7972 (tp30) cc_final: 0.7537 (tp30) REVERT: B 248 LEU cc_start: 0.9170 (mm) cc_final: 0.8951 (mm) REVERT: B 363 ARG cc_start: 0.9108 (mmm160) cc_final: 0.8676 (tpp80) REVERT: B 404 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9318 (mm) REVERT: B 405 MET cc_start: 0.9075 (mtp) cc_final: 0.8727 (mtp) REVERT: C 62 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8606 (tm-30) REVERT: C 80 MET cc_start: 0.8236 (mmt) cc_final: 0.7939 (mmm) REVERT: C 385 MET cc_start: 0.8772 (ptt) cc_final: 0.8381 (ptm) REVERT: C 391 MET cc_start: 0.8566 (ptt) cc_final: 0.7894 (ppp) REVERT: C 396 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8558 (mm-30) REVERT: C 399 MET cc_start: 0.7815 (mmp) cc_final: 0.7367 (mmt) REVERT: C 403 LYS cc_start: 0.5817 (OUTLIER) cc_final: 0.5307 (ptpp) REVERT: D 60 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8220 (t80) REVERT: D 71 GLU cc_start: 0.8631 (tp30) cc_final: 0.8360 (tp30) REVERT: D 97 ASP cc_start: 0.9062 (t0) cc_final: 0.8719 (t70) REVERT: D 98 GLN cc_start: 0.8956 (mp10) cc_final: 0.8706 (mp10) REVERT: D 214 MET cc_start: 0.9099 (ttp) cc_final: 0.8394 (mtp) REVERT: D 287 ARG cc_start: 0.9170 (mtm-85) cc_final: 0.8921 (mtm-85) REVERT: E 122 MET cc_start: 0.8004 (ptt) cc_final: 0.7788 (ptt) REVERT: E 258 MET cc_start: 0.8409 (tmm) cc_final: 0.8140 (tmm) REVERT: F 53 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6870 (pttt) REVERT: F 310 MET cc_start: 0.8973 (ppp) cc_final: 0.8501 (ppp) REVERT: F 316 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8585 (mm110) REVERT: F 351 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8890 (mtmm) REVERT: F 421 MET cc_start: 0.8983 (mmm) cc_final: 0.8618 (mmm) REVERT: F 437 TYR cc_start: 0.7091 (m-10) cc_final: 0.6481 (m-10) REVERT: G 80 MET cc_start: 0.7175 (mmm) cc_final: 0.6459 (mmm) REVERT: H 70 LYS cc_start: 0.9035 (mtmt) cc_final: 0.8591 (tptt) REVERT: H 74 LEU cc_start: 0.8830 (tp) cc_final: 0.8441 (tp) REVERT: H 165 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8515 (mmmt) REVERT: H 166 ASN cc_start: 0.8333 (m110) cc_final: 0.7450 (t0) REVERT: H 177 ARG cc_start: 0.8998 (tpp-160) cc_final: 0.8545 (tpm170) REVERT: H 203 MET cc_start: 0.7985 (mpp) cc_final: 0.7594 (mpp) REVERT: I 198 ASN cc_start: 0.7478 (t0) cc_final: 0.6743 (m-40) REVERT: J 15 HIS cc_start: 0.8175 (m90) cc_final: 0.7893 (m90) REVERT: K 8 TYR cc_start: 0.3226 (m-80) cc_final: 0.2934 (m-10) REVERT: K 59 MET cc_start: 0.7463 (tpt) cc_final: 0.6788 (tpt) REVERT: K 84 ASP cc_start: 0.7516 (m-30) cc_final: 0.7306 (m-30) REVERT: K 107 MET cc_start: 0.5665 (mpp) cc_final: 0.5395 (mpp) REVERT: K 137 PHE cc_start: 0.7669 (m-10) cc_final: 0.7463 (m-80) REVERT: K 156 MET cc_start: 0.7290 (ppp) cc_final: 0.7050 (ppp) REVERT: L 46 LEU cc_start: 0.4013 (OUTLIER) cc_final: 0.3478 (pp) REVERT: L 64 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7273 (mm) REVERT: L 159 MET cc_start: 0.2253 (ttp) cc_final: 0.1928 (ptm) REVERT: M 17 ASP cc_start: 0.8709 (m-30) cc_final: 0.8078 (t70) REVERT: M 66 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6461 (mp) REVERT: M 184 MET cc_start: 0.7025 (ptm) cc_final: 0.6463 (ppp) REVERT: U 35 TRP cc_start: 0.8953 (p-90) cc_final: 0.8704 (p-90) REVERT: U 168 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9088 (mt) REVERT: U 188 MET cc_start: 0.7097 (tpt) cc_final: 0.6743 (ppp) REVERT: U 520 MET cc_start: 0.8745 (mmm) cc_final: 0.8181 (mmm) REVERT: U 604 HIS cc_start: 0.9205 (OUTLIER) cc_final: 0.7955 (t70) REVERT: U 612 ASP cc_start: 0.8844 (m-30) cc_final: 0.8543 (m-30) REVERT: U 694 ILE cc_start: 0.8600 (tt) cc_final: 0.8351 (tt) REVERT: U 727 LYS cc_start: 0.9077 (ptpt) cc_final: 0.8773 (ptpp) REVERT: U 757 MET cc_start: 0.8519 (tmm) cc_final: 0.8210 (tmm) REVERT: U 906 LEU cc_start: 0.8521 (tp) cc_final: 0.8118 (tp) REVERT: V 38 LYS cc_start: 0.9131 (mtmt) cc_final: 0.8798 (ptpp) REVERT: V 139 MET cc_start: 0.9082 (ptm) cc_final: 0.8367 (ppp) REVERT: V 299 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8308 (tm-30) REVERT: V 301 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7847 (tm-30) REVERT: V 344 ASP cc_start: 0.7463 (t0) cc_final: 0.7115 (t70) REVERT: V 358 MET cc_start: 0.8437 (tmm) cc_final: 0.8086 (tmm) REVERT: V 482 PHE cc_start: 0.8953 (t80) cc_final: 0.8590 (t80) REVERT: V 494 MET cc_start: 0.8298 (tpt) cc_final: 0.8034 (tpp) REVERT: W 104 MET cc_start: 0.8571 (ptm) cc_final: 0.8263 (ptm) REVERT: W 198 ASP cc_start: 0.7957 (t0) cc_final: 0.7586 (m-30) REVERT: W 425 LEU cc_start: 0.9687 (mp) cc_final: 0.9457 (mp) REVERT: X 140 THR cc_start: 0.9539 (OUTLIER) cc_final: 0.9299 (p) REVERT: X 161 ASP cc_start: 0.7467 (m-30) cc_final: 0.7137 (t70) REVERT: X 162 ASP cc_start: 0.7983 (t0) cc_final: 0.7530 (t0) REVERT: X 270 LEU cc_start: 0.9497 (mm) cc_final: 0.9210 (mm) REVERT: X 304 LYS cc_start: 0.9312 (ptpt) cc_final: 0.8872 (tppt) REVERT: Y 59 LYS cc_start: 0.9183 (pttt) cc_final: 0.8947 (mmtt) REVERT: Y 73 MET cc_start: 0.7777 (ttm) cc_final: 0.7165 (mmm) REVERT: Y 105 MET cc_start: 0.7873 (mmm) cc_final: 0.7638 (mmm) REVERT: Y 250 LEU cc_start: 0.9462 (mt) cc_final: 0.9188 (mt) REVERT: Z 44 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8322 (mm-40) REVERT: Z 68 TRP cc_start: 0.8011 (p90) cc_final: 0.7226 (p90) REVERT: a 109 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6557 (tp30) REVERT: a 141 MET cc_start: 0.8440 (ppp) cc_final: 0.7989 (ppp) REVERT: a 142 LEU cc_start: 0.9039 (tp) cc_final: 0.8698 (mt) REVERT: a 278 MET cc_start: 0.9007 (mmm) cc_final: 0.8739 (mpp) REVERT: a 312 MET cc_start: 0.9152 (mtm) cc_final: 0.8765 (mtm) REVERT: a 335 TRP cc_start: 0.6888 (t60) cc_final: 0.6621 (t-100) REVERT: a 365 MET cc_start: 0.8802 (ptp) cc_final: 0.8591 (ptt) REVERT: b 15 TYR cc_start: 0.9081 (m-80) cc_final: 0.8535 (m-80) REVERT: b 16 MET cc_start: 0.8907 (tpp) cc_final: 0.8647 (tpp) REVERT: b 107 MET cc_start: 0.7867 (mmp) cc_final: 0.7432 (mmt) REVERT: c 289 ASP cc_start: 0.8921 (t0) cc_final: 0.8703 (t0) REVERT: d 160 ASP cc_start: 0.8685 (t0) cc_final: 0.8300 (t0) REVERT: d 194 LEU cc_start: 0.9252 (mt) cc_final: 0.9048 (mt) REVERT: d 309 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.8057 (p) REVERT: d 327 ASP cc_start: 0.7435 (t70) cc_final: 0.7002 (t70) REVERT: e 62 LYS cc_start: 0.8675 (pttt) cc_final: 0.8432 (pttm) REVERT: f 58 MET cc_start: 0.9364 (mmm) cc_final: 0.9079 (ppp) REVERT: f 275 MET cc_start: 0.8293 (mtm) cc_final: 0.7773 (tmm) REVERT: f 294 MET cc_start: 0.7721 (ptp) cc_final: 0.6902 (ptt) REVERT: f 297 MET cc_start: 0.9102 (mtt) cc_final: 0.8775 (mtt) REVERT: f 305 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8135 (pp) REVERT: f 309 GLU cc_start: 0.8371 (tp30) cc_final: 0.7532 (pm20) REVERT: f 416 MET cc_start: 0.8979 (mtm) cc_final: 0.8651 (mtm) REVERT: f 477 MET cc_start: 0.8505 (mmm) cc_final: 0.6796 (tpt) REVERT: f 485 LEU cc_start: 0.8799 (tp) cc_final: 0.8574 (pp) REVERT: f 744 MET cc_start: 0.9411 (mtt) cc_final: 0.9176 (mtt) REVERT: f 800 LEU cc_start: 0.9695 (mp) cc_final: 0.9464 (mp) REVERT: f 829 MET cc_start: 0.7407 (pmm) cc_final: 0.7187 (pmm) REVERT: f 866 GLN cc_start: 0.8715 (mt0) cc_final: 0.8470 (mp10) REVERT: g 94 LYS cc_start: 0.7076 (mmtp) cc_final: 0.6772 (mmtm) REVERT: g 95 LYS cc_start: 0.4208 (tppt) cc_final: 0.3790 (tttt) REVERT: g 113 ARG cc_start: 0.8357 (ttp-170) cc_final: 0.8090 (ttp-110) REVERT: g 160 GLN cc_start: 0.6874 (mp10) cc_final: 0.6358 (mt0) REVERT: u 178 TYR cc_start: 0.8801 (t80) cc_final: 0.8107 (t80) REVERT: u 218 LEU cc_start: 0.8836 (mt) cc_final: 0.8620 (tt) REVERT: u 244 VAL cc_start: 0.9496 (OUTLIER) cc_final: 0.9278 (m) REVERT: u 266 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8751 (tp) REVERT: u 285 LYS cc_start: 0.7856 (mttt) cc_final: 0.7271 (mmmt) outliers start: 217 outliers final: 179 residues processed: 969 average time/residue: 0.6807 time to fit residues: 1136.9385 Evaluate side-chains 985 residues out of total 7738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 788 time to evaluate : 6.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 420 TYR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 351 LYS Chi-restraints excluded: chain G residue 23 TYR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 163 HIS Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 12 PHE Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain U residue 168 LEU Chi-restraints excluded: chain U residue 185 MET Chi-restraints excluded: chain U residue 244 MET Chi-restraints excluded: chain U residue 252 LEU Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 366 HIS Chi-restraints excluded: chain U residue 367 THR Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 604 HIS Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 835 ILE Chi-restraints excluded: chain U residue 921 ILE Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 135 LEU Chi-restraints excluded: chain V residue 144 ASP Chi-restraints excluded: chain V residue 147 PHE Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 176 MET Chi-restraints excluded: chain V residue 194 LYS Chi-restraints excluded: chain V residue 212 TYR Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 263 LEU Chi-restraints excluded: chain V residue 303 SER Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 338 LEU Chi-restraints excluded: chain V residue 346 LEU Chi-restraints excluded: chain V residue 394 LEU Chi-restraints excluded: chain V residue 418 SER Chi-restraints excluded: chain V residue 422 ILE Chi-restraints excluded: chain V residue 443 ARG Chi-restraints excluded: chain W residue 60 MET Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 351 TRP Chi-restraints excluded: chain W residue 427 ASP Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 256 LEU Chi-restraints excluded: chain X residue 388 PHE Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 416 ASN Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 136 HIS Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 220 VAL Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 92 VAL Chi-restraints excluded: chain Z residue 135 THR Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 182 THR Chi-restraints excluded: chain Z residue 227 ILE Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 231 GLN Chi-restraints excluded: chain Z residue 266 ILE Chi-restraints excluded: chain a residue 60 TYR Chi-restraints excluded: chain a residue 109 GLU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 275 LEU Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 310 LEU Chi-restraints excluded: chain a residue 343 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain c residue 32 TYR Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 118 PHE Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 179 SER Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain d residue 108 ASN Chi-restraints excluded: chain d residue 242 ASN Chi-restraints excluded: chain d residue 245 PHE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 177 GLU Chi-restraints excluded: chain f residue 231 LEU Chi-restraints excluded: chain f residue 256 PHE Chi-restraints excluded: chain f residue 266 LEU Chi-restraints excluded: chain f residue 305 LEU Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 510 SER Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 852 VAL Chi-restraints excluded: chain f residue 898 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 167 ILE Chi-restraints excluded: chain u residue 182 PHE Chi-restraints excluded: chain u residue 244 VAL Chi-restraints excluded: chain u residue 266 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 152 optimal weight: 6.9990 chunk 683 optimal weight: 0.8980 chunk 340 optimal weight: 40.0000 chunk 66 optimal weight: 4.9990 chunk 388 optimal weight: 5.9990 chunk 867 optimal weight: 7.9990 chunk 529 optimal weight: 6.9990 chunk 767 optimal weight: 2.9990 chunk 833 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 503 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 768 GLN ** V 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 7 GLN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 108 ASN ** d 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.085076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.068179 restraints weight = 371062.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.070270 restraints weight = 207263.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.070993 restraints weight = 137776.100| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.7586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 71563 Z= 0.236 Angle : 0.782 14.916 96729 Z= 0.384 Chirality : 0.045 0.303 11063 Planarity : 0.004 0.073 12470 Dihedral : 6.902 162.743 9840 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.28 % Favored : 93.39 % Rotamer: Outliers : 2.82 % Allowed : 24.20 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.09), residues: 8837 helix: 0.76 (0.08), residues: 4835 sheet: -0.78 (0.17), residues: 936 loop : -0.98 (0.12), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP a 255 HIS 0.015 0.001 HIS U 754 PHE 0.028 0.002 PHE W 309 TYR 0.028 0.002 TYR f 681 ARG 0.014 0.001 ARG C 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29419.27 seconds wall clock time: 508 minutes 52.64 seconds (30532.64 seconds total)