Starting phenix.real_space_refine on Fri Sep 27 19:57:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xt9_10617/09_2024/6xt9_10617.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xt9_10617/09_2024/6xt9_10617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xt9_10617/09_2024/6xt9_10617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xt9_10617/09_2024/6xt9_10617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xt9_10617/09_2024/6xt9_10617.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xt9_10617/09_2024/6xt9_10617.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 10811 2.51 5 N 2888 2.21 5 O 3127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16916 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4378 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 38, 'TRANS': 528} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3069 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 10, 'TRANS': 385} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 61 Chain: "H" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3192 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 5834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5834 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 31, 'TRANS': 735} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 132 Chain: "J" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 443 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Time building chain proxies: 9.44, per 1000 atoms: 0.56 Number of scatterers: 16916 At special positions: 0 Unit cell: (141.24, 160.5, 139.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3127 8.00 N 2888 7.00 C 10811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.06 Conformation dependent library (CDL) restraints added in 2.2 seconds 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4144 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 25 sheets defined 40.4% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 132 through 140 removed outlier: 3.938A pdb=" N LEU A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 removed outlier: 3.509A pdb=" N LEU A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 431 through 436 removed outlier: 3.675A pdb=" N VAL A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 444 removed outlier: 3.587A pdb=" N ARG A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 472 removed outlier: 3.891A pdb=" N MET A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.944A pdb=" N ILE D 39 " --> pdb=" O GLN D 35 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 41 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.565A pdb=" N LYS D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 81 removed outlier: 3.658A pdb=" N GLN D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 removed outlier: 4.004A pdb=" N GLU D 88 " --> pdb=" O GLN D 84 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 removed outlier: 4.215A pdb=" N ALA D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER D 110 " --> pdb=" O GLN D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 131 removed outlier: 3.541A pdb=" N ALA D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 147 removed outlier: 3.617A pdb=" N LEU D 141 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY D 142 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 165 removed outlier: 3.963A pdb=" N ASP D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU D 164 " --> pdb=" O ASN D 160 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 182 removed outlier: 3.762A pdb=" N ILE D 172 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 174 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 179 " --> pdb=" O GLY D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 198 removed outlier: 4.162A pdb=" N GLU D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 190 " --> pdb=" O LYS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.598A pdb=" N LEU D 205 " --> pdb=" O ASN D 201 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 232 removed outlier: 3.790A pdb=" N GLU D 223 " --> pdb=" O GLN D 219 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 248 removed outlier: 3.669A pdb=" N LEU D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA D 241 " --> pdb=" O LYS D 237 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN D 247 " --> pdb=" O GLY D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 263 removed outlier: 3.686A pdb=" N THR D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.533A pdb=" N ASN D 275 " --> pdb=" O PRO D 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY D 282 " --> pdb=" O MET D 278 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS D 283 " --> pdb=" O CYS D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 300 removed outlier: 3.786A pdb=" N ILE D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA D 296 " --> pdb=" O CYS D 292 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 299 " --> pdb=" O ARG D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 removed outlier: 3.857A pdb=" N TYR D 308 " --> pdb=" O TRP D 304 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 315 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 332 removed outlier: 3.532A pdb=" N PHE D 324 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N HIS D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE D 326 " --> pdb=" O SER D 322 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN D 332 " --> pdb=" O SER D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 350 removed outlier: 3.564A pdb=" N ALA D 345 " --> pdb=" O TYR D 341 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 346 " --> pdb=" O MET D 342 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN D 350 " --> pdb=" O VAL D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 367 removed outlier: 3.507A pdb=" N ARG D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 383 removed outlier: 3.835A pdb=" N ASN D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU D 381 " --> pdb=" O ASN D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'D' and resid 407 through 422 removed outlier: 4.165A pdb=" N LEU D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP D 414 " --> pdb=" O SER D 410 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN D 422 " --> pdb=" O VAL D 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 17 removed outlier: 3.545A pdb=" N ARG H 17 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 30 removed outlier: 4.165A pdb=" N ASP H 25 " --> pdb=" O GLN H 21 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET H 30 " --> pdb=" O LEU H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 50 removed outlier: 3.540A pdb=" N LEU H 48 " --> pdb=" O LYS H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 189 removed outlier: 3.510A pdb=" N TYR H 188 " --> pdb=" O ALA H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 194 removed outlier: 3.807A pdb=" N GLU H 193 " --> pdb=" O ILE H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 210 removed outlier: 3.540A pdb=" N ALA H 199 " --> pdb=" O ASP H 195 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP H 201 " --> pdb=" O LYS H 197 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU H 202 " --> pdb=" O THR H 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 229 removed outlier: 3.521A pdb=" N GLY H 222 " --> pdb=" O LYS H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 243 removed outlier: 4.277A pdb=" N LYS H 239 " --> pdb=" O GLU H 235 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER H 240 " --> pdb=" O LYS H 236 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA H 241 " --> pdb=" O GLN H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 261 removed outlier: 3.605A pdb=" N PHE H 251 " --> pdb=" O MET H 247 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS H 256 " --> pdb=" O LEU H 252 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL H 259 " --> pdb=" O ALA H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 274 removed outlier: 3.866A pdb=" N ASN H 269 " --> pdb=" O VAL H 265 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU H 270 " --> pdb=" O THR H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 277 No H-bonds generated for 'chain 'H' and resid 275 through 277' Processing helix chain 'H' and resid 281 through 292 removed outlier: 3.671A pdb=" N LEU H 285 " --> pdb=" O GLU H 281 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA H 289 " --> pdb=" O LEU H 285 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE H 291 " --> pdb=" O GLY H 287 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR H 292 " --> pdb=" O ILE H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 302 removed outlier: 3.675A pdb=" N ALA H 302 " --> pdb=" O MET H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 307 Processing helix chain 'H' and resid 315 through 318 removed outlier: 3.548A pdb=" N ALA H 318 " --> pdb=" O HIS H 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 315 through 318' Processing helix chain 'H' and resid 319 through 324 Processing helix chain 'H' and resid 333 through 345 removed outlier: 3.602A pdb=" N TYR H 339 " --> pdb=" O ALA H 335 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG H 341 " --> pdb=" O ARG H 337 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU H 342 " --> pdb=" O PHE H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 363 removed outlier: 3.522A pdb=" N ASN H 354 " --> pdb=" O GLY H 350 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS H 360 " --> pdb=" O LEU H 356 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE H 361 " --> pdb=" O GLY H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 378 removed outlier: 4.545A pdb=" N THR H 371 " --> pdb=" O ASP H 367 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER H 372 " --> pdb=" O MET H 368 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE H 373 " --> pdb=" O THR H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 401 removed outlier: 4.280A pdb=" N ASP H 388 " --> pdb=" O GLU H 384 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL H 389 " --> pdb=" O GLU H 385 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS H 395 " --> pdb=" O TYR H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 402 through 417 removed outlier: 3.719A pdb=" N GLN H 408 " --> pdb=" O ASN H 404 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE H 410 " --> pdb=" O ALA H 406 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG H 411 " --> pdb=" O HIS H 407 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 420 through 435 removed outlier: 3.790A pdb=" N ASN H 425 " --> pdb=" O ALA H 421 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN H 426 " --> pdb=" O GLU H 422 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL H 429 " --> pdb=" O ASN H 425 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU H 430 " --> pdb=" O ASN H 426 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N MET H 432 " --> pdb=" O ALA H 428 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS H 434 " --> pdb=" O LEU H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 436 through 449 removed outlier: 3.653A pdb=" N ALA H 442 " --> pdb=" O GLU H 438 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU H 443 " --> pdb=" O GLN H 439 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN H 445 " --> pdb=" O ARG H 441 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER H 449 " --> pdb=" O GLN H 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 462 removed outlier: 3.549A pdb=" N ALA H 462 " --> pdb=" O HIS H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 484 removed outlier: 3.630A pdb=" N VAL H 476 " --> pdb=" O GLN H 472 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA H 478 " --> pdb=" O SER H 474 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU H 482 " --> pdb=" O ALA H 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 493 removed outlier: 3.911A pdb=" N GLN H 492 " --> pdb=" O HIS H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 504 removed outlier: 3.690A pdb=" N GLN H 500 " --> pdb=" O LYS H 496 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS H 501 " --> pdb=" O GLN H 497 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA H 503 " --> pdb=" O ARG H 499 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET H 504 " --> pdb=" O GLN H 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 146 removed outlier: 3.663A pdb=" N GLY I 145 " --> pdb=" O SER I 142 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL I 146 " --> pdb=" O PHE I 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 142 through 146' Processing helix chain 'I' and resid 401 through 414 removed outlier: 3.605A pdb=" N THR I 405 " --> pdb=" O VAL I 401 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASP I 410 " --> pdb=" O GLU I 406 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU I 411 " --> pdb=" O ARG I 407 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN I 412 " --> pdb=" O GLU I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 558 through 562 Processing helix chain 'I' and resid 609 through 625 removed outlier: 4.187A pdb=" N ASN I 614 " --> pdb=" O TRP I 610 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU I 615 " --> pdb=" O LEU I 611 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU I 625 " --> pdb=" O GLN I 621 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 660 removed outlier: 3.987A pdb=" N GLU I 644 " --> pdb=" O ILE I 640 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU I 647 " --> pdb=" O GLN I 643 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU I 648 " --> pdb=" O GLU I 644 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP I 650 " --> pdb=" O PHE I 646 " (cutoff:3.500A) Processing helix chain 'I' and resid 663 through 684 removed outlier: 3.553A pdb=" N GLU I 668 " --> pdb=" O GLU I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 696 through 709 removed outlier: 3.590A pdb=" N ASP I 700 " --> pdb=" O ASP I 696 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY I 701 " --> pdb=" O THR I 697 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR I 702 " --> pdb=" O LEU I 698 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL I 706 " --> pdb=" O THR I 702 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE I 707 " --> pdb=" O TYR I 703 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU I 709 " --> pdb=" O GLN I 705 " (cutoff:3.500A) Processing helix chain 'I' and resid 712 through 742 removed outlier: 3.899A pdb=" N ASN I 716 " --> pdb=" O ALA I 712 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN I 717 " --> pdb=" O VAL I 713 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG I 726 " --> pdb=" O GLN I 722 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU I 737 " --> pdb=" O LEU I 733 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA I 739 " --> pdb=" O ILE I 735 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU I 740 " --> pdb=" O LEU I 736 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN I 742 " --> pdb=" O ILE I 738 " (cutoff:3.500A) Processing helix chain 'I' and resid 747 through 756 removed outlier: 3.605A pdb=" N ALA I 754 " --> pdb=" O ALA I 750 " (cutoff:3.500A) Processing helix chain 'I' and resid 767 through 780 removed outlier: 3.830A pdb=" N ASP I 773 " --> pdb=" O GLU I 769 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA I 774 " --> pdb=" O GLU I 770 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS I 778 " --> pdb=" O ALA I 774 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU I 780 " --> pdb=" O ILE I 776 " (cutoff:3.500A) Processing helix chain 'I' and resid 788 through 799 removed outlier: 3.733A pdb=" N LEU I 795 " --> pdb=" O GLN I 791 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN I 798 " --> pdb=" O ASN I 794 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 80 removed outlier: 3.952A pdb=" N ASN J 75 " --> pdb=" O GLN J 71 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE J 77 " --> pdb=" O ALA J 73 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN J 79 " --> pdb=" O ASN J 75 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN J 80 " --> pdb=" O THR J 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 29 removed outlier: 5.410A pdb=" N ASP A 25 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 401 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A 27 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 398 " --> pdb=" O MET A 390 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A 400 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 388 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ASP A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TYR A 381 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER A 375 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44 removed outlier: 3.646A pdb=" N ALA A 44 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A 78 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS A 72 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VAL A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 92 removed outlier: 3.664A pdb=" N ALA A 88 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 114 " --> pdb=" O TYR A 121 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR A 121 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 207 removed outlier: 3.689A pdb=" N THR A 202 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A 222 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 230 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 240 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 253 removed outlier: 3.500A pdb=" N CYS A 267 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASN A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 274 " --> pdb=" O TYR A 284 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR A 284 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 297 removed outlier: 6.305A pdb=" N GLY A 305 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU A 295 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 303 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 311 Processing sheet with id=AA8, first strand: chain 'A' and resid 330 through 337 removed outlier: 3.654A pdb=" N ASN A 334 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 486 through 490 removed outlier: 3.707A pdb=" N HIS A 489 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 486 through 490 removed outlier: 3.707A pdb=" N HIS A 489 " --> pdb=" O THR A 502 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 501 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.814A pdb=" N VAL A 519 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 25 through 28 removed outlier: 3.561A pdb=" N ILE I 41 " --> pdb=" O CYS I 26 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE I 51 " --> pdb=" O LEU I 70 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU I 70 " --> pdb=" O ILE I 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 78 through 82 removed outlier: 4.150A pdb=" N GLN I 80 " --> pdb=" O LEU I 98 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU I 98 " --> pdb=" O GLN I 80 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU I 95 " --> pdb=" O TYR I 106 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS I 102 " --> pdb=" O HIS I 99 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS I 124 " --> pdb=" O SER I 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 78 through 82 removed outlier: 4.150A pdb=" N GLN I 80 " --> pdb=" O LEU I 98 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU I 98 " --> pdb=" O GLN I 80 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU I 95 " --> pdb=" O TYR I 106 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS I 102 " --> pdb=" O HIS I 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 135 through 137 removed outlier: 7.345A pdb=" N GLN I 155 " --> pdb=" O CYS I 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 140 through 141 Processing sheet with id=AB8, first strand: chain 'I' and resid 160 through 164 removed outlier: 3.840A pdb=" N PHE I 171 " --> pdb=" O VAL I 163 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 184 through 186 Processing sheet with id=AC1, first strand: chain 'I' and resid 245 through 252 removed outlier: 4.013A pdb=" N ASP I 247 " --> pdb=" O LEU I 263 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU I 263 " --> pdb=" O ASP I 247 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL I 251 " --> pdb=" O SER I 259 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL I 262 " --> pdb=" O PHE I 269 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N CYS I 270 " --> pdb=" O ARG I 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 290 through 291 Processing sheet with id=AC3, first strand: chain 'I' and resid 332 through 336 removed outlier: 3.776A pdb=" N ARG I 334 " --> pdb=" O VAL I 346 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY I 336 " --> pdb=" O VAL I 344 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL I 344 " --> pdb=" O GLY I 336 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 430 through 432 removed outlier: 3.690A pdb=" N VAL I 440 " --> pdb=" O VAL I 489 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 472 through 473 removed outlier: 3.628A pdb=" N LEU I 457 " --> pdb=" O PHE I 472 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS I 454 " --> pdb=" O SER I 509 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER I 509 " --> pdb=" O LYS I 454 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 472 through 473 removed outlier: 3.628A pdb=" N LEU I 457 " --> pdb=" O PHE I 472 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS I 454 " --> pdb=" O SER I 509 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER I 509 " --> pdb=" O LYS I 454 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 546 through 550 removed outlier: 3.520A pdb=" N HIS I 546 " --> pdb=" O SER I 603 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1683 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: 5.29 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5372 1.34 - 1.46: 2812 1.46 - 1.57: 8938 1.57 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 17260 Sorted by residual: bond pdb=" C ASN D 371 " pdb=" N PRO D 372 " ideal model delta sigma weight residual 1.330 1.367 -0.036 1.23e-02 6.61e+03 8.76e+00 bond pdb=" N ASP I 317 " pdb=" CA ASP I 317 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.77e+00 bond pdb=" N PRO A 419 " pdb=" CA PRO A 419 " ideal model delta sigma weight residual 1.473 1.453 0.020 8.50e-03 1.38e+04 5.58e+00 bond pdb=" N GLU A 410 " pdb=" CA GLU A 410 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.30e+00 bond pdb=" C THR I 688 " pdb=" N PRO I 689 " ideal model delta sigma weight residual 1.335 1.357 -0.022 9.40e-03 1.13e+04 5.27e+00 ... (remaining 17255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 23001 3.13 - 6.27: 356 6.27 - 9.40: 58 9.40 - 12.54: 6 12.54 - 15.67: 2 Bond angle restraints: 23423 Sorted by residual: angle pdb=" N PRO A 419 " pdb=" CA PRO A 419 " pdb=" CB PRO A 419 " ideal model delta sigma weight residual 101.88 110.61 -8.73 1.01e+00 9.80e-01 7.48e+01 angle pdb=" N PRO A 418 " pdb=" CA PRO A 418 " pdb=" CB PRO A 418 " ideal model delta sigma weight residual 103.08 111.26 -8.18 9.70e-01 1.06e+00 7.11e+01 angle pdb=" N PRO I 369 " pdb=" CA PRO I 369 " pdb=" CB PRO I 369 " ideal model delta sigma weight residual 103.25 111.37 -8.12 1.05e+00 9.07e-01 5.98e+01 angle pdb=" N PRO A 417 " pdb=" CA PRO A 417 " pdb=" CB PRO A 417 " ideal model delta sigma weight residual 103.08 109.96 -6.88 9.70e-01 1.06e+00 5.02e+01 angle pdb=" N PRO I 403 " pdb=" CA PRO I 403 " pdb=" CB PRO I 403 " ideal model delta sigma weight residual 103.51 110.19 -6.68 9.60e-01 1.09e+00 4.84e+01 ... (remaining 23418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 9081 17.85 - 35.70: 1065 35.70 - 53.56: 188 53.56 - 71.41: 45 71.41 - 89.26: 23 Dihedral angle restraints: 10402 sinusoidal: 4005 harmonic: 6397 Sorted by residual: dihedral pdb=" CA VAL I 437 " pdb=" C VAL I 437 " pdb=" N PRO I 438 " pdb=" CA PRO I 438 " ideal model delta harmonic sigma weight residual -180.00 -111.84 -68.16 0 5.00e+00 4.00e-02 1.86e+02 dihedral pdb=" CA ALA I 633 " pdb=" C ALA I 633 " pdb=" N CYS I 634 " pdb=" CA CYS I 634 " ideal model delta harmonic sigma weight residual 180.00 127.53 52.47 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA GLN H 211 " pdb=" C GLN H 211 " pdb=" N TYR H 212 " pdb=" CA TYR H 212 " ideal model delta harmonic sigma weight residual 180.00 141.49 38.51 0 5.00e+00 4.00e-02 5.93e+01 ... (remaining 10399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2421 0.089 - 0.178: 233 0.178 - 0.266: 30 0.266 - 0.355: 2 0.355 - 0.444: 2 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CB ILE I 534 " pdb=" CA ILE I 534 " pdb=" CG1 ILE I 534 " pdb=" CG2 ILE I 534 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" CB VAL I 437 " pdb=" CA VAL I 437 " pdb=" CG1 VAL I 437 " pdb=" CG2 VAL I 437 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CA PRO I 369 " pdb=" N PRO I 369 " pdb=" C PRO I 369 " pdb=" CB PRO I 369 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2685 not shown) Planarity restraints: 3011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 409 " -0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C VAL A 409 " 0.089 2.00e-02 2.50e+03 pdb=" O VAL A 409 " -0.034 2.00e-02 2.50e+03 pdb=" N GLU A 410 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL I 437 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO I 438 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO I 438 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO I 438 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO I 463 " -0.057 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO I 464 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO I 464 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO I 464 " -0.049 5.00e-02 4.00e+02 ... (remaining 3008 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4811 2.81 - 3.33: 15432 3.33 - 3.85: 27153 3.85 - 4.38: 30345 4.38 - 4.90: 51167 Nonbonded interactions: 128908 Sorted by model distance: nonbonded pdb=" O SER D 86 " pdb=" OG SER D 86 " model vdw 2.285 3.040 nonbonded pdb=" O VAL I 444 " pdb=" OG1 THR I 484 " model vdw 2.294 3.040 nonbonded pdb=" OG SER I 156 " pdb=" OD1 ASP I 158 " model vdw 2.298 3.040 nonbonded pdb=" O PHE I 86 " pdb=" OH TYR I 127 " model vdw 2.299 3.040 nonbonded pdb=" O GLY I 767 " pdb=" OG1 THR I 771 " model vdw 2.306 3.040 ... (remaining 128903 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.050 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.005 0.072 17260 Z= 0.344 Angle : 1.005 15.672 23423 Z= 0.564 Chirality : 0.057 0.444 2688 Planarity : 0.007 0.106 3011 Dihedral : 16.304 89.260 6258 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.41 % Favored : 90.31 % Rotamer: Outliers : 0.34 % Allowed : 10.91 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.24 % 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: -5.57 (0.13), residues: 2167 helix: -4.21 (0.09), residues: 813 sheet: -2.87 (0.22), residues: 416 loop : -3.45 (0.16), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 139 HIS 0.008 0.001 HIS H 192 PHE 0.032 0.002 PHE I 632 TYR 0.025 0.002 TYR D 361 ARG 0.005 0.000 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 279 time to evaluate : 1.773 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: A 160 ARG cc_start: 0.8805 (ttp-170) cc_final: 0.8188 (mmt180) REVERT: A 347 MET cc_start: 0.8346 (mpp) cc_final: 0.8139 (mpp) REVERT: A 578 LEU cc_start: 0.8785 (pp) cc_final: 0.8360 (pp) REVERT: D 246 MET cc_start: 0.8110 (mmt) cc_final: 0.7568 (mmm) REVERT: D 251 ASP cc_start: 0.7759 (m-30) cc_final: 0.7406 (m-30) REVERT: D 260 ARG cc_start: 0.8655 (mtt180) cc_final: 0.8412 (mtt-85) REVERT: D 295 ARG cc_start: 0.8515 (ttt180) cc_final: 0.8304 (ttt90) REVERT: D 343 LEU cc_start: 0.9462 (mm) cc_final: 0.9177 (mm) REVERT: D 361 TYR cc_start: 0.6912 (t80) cc_final: 0.6679 (t80) REVERT: H 53 TYR cc_start: 0.8538 (t80) cc_final: 0.8137 (t80) REVERT: H 186 PHE cc_start: 0.8562 (t80) cc_final: 0.8183 (t80) REVERT: H 190 PHE cc_start: 0.8989 (m-80) cc_final: 0.8654 (m-80) REVERT: H 225 TYR cc_start: 0.8806 (m-10) cc_final: 0.8377 (m-10) REVERT: H 286 CYS cc_start: 0.8593 (t) cc_final: 0.8255 (t) REVERT: H 334 ILE cc_start: 0.9118 (mt) cc_final: 0.8910 (tt) REVERT: H 480 LYS cc_start: 0.9197 (mttt) cc_final: 0.8601 (mmmm) REVERT: I 98 LEU cc_start: 0.8625 (tp) cc_final: 0.8364 (tt) REVERT: I 123 MET cc_start: 0.7284 (mmp) cc_final: 0.7035 (mmp) REVERT: I 138 MET cc_start: 0.7847 (ptm) cc_final: 0.7587 (ptp) REVERT: I 284 ASP cc_start: 0.8432 (p0) cc_final: 0.8188 (p0) REVERT: I 477 MET cc_start: 0.3765 (mmt) cc_final: 0.1972 (mmt) REVERT: I 501 GLU cc_start: 0.8739 (pp20) cc_final: 0.8177 (pp20) REVERT: I 535 CYS cc_start: 0.7271 (t) cc_final: 0.6541 (p) REVERT: I 711 ASP cc_start: 0.9109 (m-30) cc_final: 0.8668 (p0) REVERT: J 69 MET cc_start: 0.8594 (tmm) cc_final: 0.7976 (tmm) REVERT: J 70 HIS cc_start: 0.8170 (t-90) cc_final: 0.7900 (t70) outliers start: 6 outliers final: 3 residues processed: 285 average time/residue: 0.2820 time to fit residues: 119.7127 Evaluate side-chains 204 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 201 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 230 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 55 optimal weight: 0.0570 chunk 109 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 125 optimal weight: 0.5980 chunk 195 optimal weight: 5.9990 overall best weight: 1.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 316 HIS A 504 HIS A 581 HIS D 40 HIS D 103 ASN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 HIS D 366 HIS D 371 ASN D 377 ASN D 384 ASN H 325 ASN ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 419 ASN H 500 GLN I 55 HIS I 120 GLN I 166 GLN I 307 ASN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 515 ASN I 553 ASN ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 677 GLN I 719 ASN I 748 GLN I 760 GLN ** I 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17260 Z= 0.273 Angle : 0.708 14.391 23423 Z= 0.370 Chirality : 0.044 0.228 2688 Planarity : 0.006 0.098 3011 Dihedral : 6.364 59.450 2338 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.54 % Favored : 91.32 % Rotamer: Outliers : 2.59 % Allowed : 16.19 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.10 % 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: -4.10 (0.15), residues: 2167 helix: -2.30 (0.14), residues: 870 sheet: -2.35 (0.23), residues: 384 loop : -3.22 (0.18), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 610 HIS 0.011 0.001 HIS D 366 PHE 0.018 0.002 PHE A 521 TYR 0.030 0.002 TYR H 304 ARG 0.005 0.000 ARG I 669 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 227 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.8228 (mpp) cc_final: 0.7859 (mpp) REVERT: A 570 ARG cc_start: 0.7657 (mmm-85) cc_final: 0.7365 (mmm-85) REVERT: D 246 MET cc_start: 0.8217 (mmt) cc_final: 0.7744 (mmm) REVERT: D 251 ASP cc_start: 0.7612 (m-30) cc_final: 0.7305 (m-30) REVERT: D 260 ARG cc_start: 0.8753 (mtt180) cc_final: 0.8477 (mtt-85) REVERT: D 337 MET cc_start: 0.8885 (tpp) cc_final: 0.7814 (tpp) REVERT: D 339 GLU cc_start: 0.8652 (mp0) cc_final: 0.8028 (mp0) REVERT: D 373 LEU cc_start: 0.7593 (mt) cc_final: 0.7358 (pp) REVERT: H 61 GLN cc_start: 0.6374 (mm-40) cc_final: 0.5167 (mm-40) REVERT: H 186 PHE cc_start: 0.8577 (t80) cc_final: 0.8066 (t80) REVERT: H 190 PHE cc_start: 0.9108 (m-80) cc_final: 0.8529 (m-80) REVERT: H 230 MET cc_start: 0.7542 (mtp) cc_final: 0.6659 (mpp) REVERT: H 295 MET cc_start: 0.9332 (mmt) cc_final: 0.8923 (mpp) REVERT: H 479 GLN cc_start: 0.8887 (tp40) cc_final: 0.8638 (tp40) REVERT: H 480 LYS cc_start: 0.9181 (mttt) cc_final: 0.8665 (mmmm) REVERT: I 123 MET cc_start: 0.7237 (mmp) cc_final: 0.7033 (mmp) REVERT: I 138 MET cc_start: 0.8190 (ptm) cc_final: 0.7788 (ptp) REVERT: I 239 LEU cc_start: 0.8717 (tp) cc_final: 0.8293 (mt) REVERT: I 284 ASP cc_start: 0.8359 (p0) cc_final: 0.8156 (p0) REVERT: I 477 MET cc_start: 0.4125 (mmt) cc_final: 0.2426 (mmt) REVERT: I 481 LEU cc_start: 0.5627 (OUTLIER) cc_final: 0.5123 (pt) REVERT: I 535 CYS cc_start: 0.6983 (t) cc_final: 0.6143 (p) REVERT: I 711 ASP cc_start: 0.9162 (m-30) cc_final: 0.8671 (p0) REVERT: I 770 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6484 (tt0) REVERT: J 43 GLU cc_start: 0.9120 (pm20) cc_final: 0.8893 (pm20) REVERT: J 69 MET cc_start: 0.8273 (tmm) cc_final: 0.7678 (tmm) REVERT: J 70 HIS cc_start: 0.7903 (t-90) cc_final: 0.7630 (t70) REVERT: J 71 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8075 (tm-30) outliers start: 46 outliers final: 24 residues processed: 259 average time/residue: 0.2670 time to fit residues: 107.0965 Evaluate side-chains 221 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 196 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 425 ASN Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 289 CYS Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 590 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 chunk 211 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 193 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 156 optimal weight: 0.0470 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 HIS D 165 ASN D 309 ASN ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 339 HIS ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17260 Z= 0.174 Angle : 0.648 11.060 23423 Z= 0.329 Chirality : 0.042 0.220 2688 Planarity : 0.005 0.093 3011 Dihedral : 5.740 57.664 2338 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.08 % Favored : 91.83 % Rotamer: Outliers : 2.70 % Allowed : 18.44 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.10 % 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: -3.32 (0.17), residues: 2167 helix: -1.35 (0.16), residues: 864 sheet: -2.04 (0.24), residues: 379 loop : -3.06 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 610 HIS 0.011 0.001 HIS A 581 PHE 0.019 0.001 PHE H 238 TYR 0.019 0.001 TYR H 304 ARG 0.004 0.000 ARG D 295 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 228 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LEU cc_start: 0.8848 (tp) cc_final: 0.8634 (pp) REVERT: A 326 MET cc_start: 0.8261 (mpp) cc_final: 0.7878 (mpp) REVERT: A 581 HIS cc_start: 0.7677 (OUTLIER) cc_final: 0.6806 (p-80) REVERT: A 584 MET cc_start: 0.8364 (ppp) cc_final: 0.7484 (ppp) REVERT: D 31 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8339 (tt) REVERT: D 203 GLU cc_start: 0.8359 (mp0) cc_final: 0.7956 (mp0) REVERT: D 260 ARG cc_start: 0.8744 (mtt180) cc_final: 0.8458 (mtt-85) REVERT: D 337 MET cc_start: 0.8752 (tpp) cc_final: 0.7746 (tpp) REVERT: D 339 GLU cc_start: 0.8606 (mp0) cc_final: 0.8074 (mp0) REVERT: D 361 TYR cc_start: 0.7895 (t80) cc_final: 0.7633 (t80) REVERT: H 186 PHE cc_start: 0.8600 (t80) cc_final: 0.8055 (t80) REVERT: H 190 PHE cc_start: 0.9086 (m-80) cc_final: 0.8477 (m-80) REVERT: H 230 MET cc_start: 0.7242 (mtp) cc_final: 0.6597 (mpp) REVERT: H 295 MET cc_start: 0.9307 (mmt) cc_final: 0.8917 (mpp) REVERT: H 377 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8556 (mm) REVERT: H 405 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9119 (tt) REVERT: H 480 LYS cc_start: 0.9199 (mttt) cc_final: 0.8694 (mmmm) REVERT: H 482 GLU cc_start: 0.8376 (tt0) cc_final: 0.7854 (mt-10) REVERT: I 123 MET cc_start: 0.7278 (mmp) cc_final: 0.6994 (mmp) REVERT: I 138 MET cc_start: 0.8191 (ptm) cc_final: 0.7705 (ptp) REVERT: I 239 LEU cc_start: 0.8698 (tp) cc_final: 0.8388 (mt) REVERT: I 477 MET cc_start: 0.4187 (mmt) cc_final: 0.2608 (mmt) REVERT: I 481 LEU cc_start: 0.5481 (OUTLIER) cc_final: 0.4884 (pt) REVERT: I 535 CYS cc_start: 0.6902 (t) cc_final: 0.6494 (t) REVERT: I 580 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7674 (t80) REVERT: I 582 PHE cc_start: 0.5192 (m-80) cc_final: 0.4755 (m-80) REVERT: I 673 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: I 711 ASP cc_start: 0.9134 (m-30) cc_final: 0.8642 (p0) REVERT: J 43 GLU cc_start: 0.9029 (pm20) cc_final: 0.8718 (pm20) REVERT: J 71 GLN cc_start: 0.8268 (tm-30) cc_final: 0.8014 (tm-30) outliers start: 48 outliers final: 21 residues processed: 262 average time/residue: 0.2539 time to fit residues: 104.2017 Evaluate side-chains 229 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 425 ASN Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain J residue 45 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 21 optimal weight: 0.0870 chunk 93 optimal weight: 50.0000 chunk 131 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 102 optimal weight: 0.0030 chunk 186 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 2.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 581 HIS D 155 GLN D 178 HIS D 366 HIS ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 448 ASN ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17260 Z= 0.307 Angle : 0.694 12.159 23423 Z= 0.352 Chirality : 0.044 0.216 2688 Planarity : 0.005 0.090 3011 Dihedral : 5.754 57.072 2338 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.37 % Favored : 90.54 % Rotamer: Outliers : 3.65 % Allowed : 20.24 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.10 % 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: -2.97 (0.17), residues: 2167 helix: -0.92 (0.17), residues: 875 sheet: -1.92 (0.25), residues: 372 loop : -3.02 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 610 HIS 0.013 0.001 HIS A 581 PHE 0.019 0.002 PHE A 521 TYR 0.021 0.002 TYR H 304 ARG 0.003 0.000 ARG I 669 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 198 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.8338 (mpp) cc_final: 0.7811 (mpp) REVERT: A 570 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.7392 (mmm-85) REVERT: A 581 HIS cc_start: 0.7796 (OUTLIER) cc_final: 0.6799 (p-80) REVERT: A 584 MET cc_start: 0.8308 (ppp) cc_final: 0.7343 (ppp) REVERT: D 173 MET cc_start: 0.8881 (mmm) cc_final: 0.8531 (mmm) REVERT: D 203 GLU cc_start: 0.8408 (mp0) cc_final: 0.7998 (mp0) REVERT: D 260 ARG cc_start: 0.8788 (mtt180) cc_final: 0.8525 (mtt-85) REVERT: D 337 MET cc_start: 0.8795 (tpp) cc_final: 0.7933 (tpp) REVERT: D 339 GLU cc_start: 0.8620 (mp0) cc_final: 0.8090 (mp0) REVERT: D 361 TYR cc_start: 0.8220 (t80) cc_final: 0.7887 (t80) REVERT: H 186 PHE cc_start: 0.8674 (t80) cc_final: 0.8114 (t80) REVERT: H 190 PHE cc_start: 0.9186 (m-80) cc_final: 0.8597 (m-80) REVERT: H 230 MET cc_start: 0.7209 (mtp) cc_final: 0.6966 (ttm) REVERT: H 295 MET cc_start: 0.9342 (mmt) cc_final: 0.8839 (mpp) REVERT: H 298 MET cc_start: 0.8542 (tmm) cc_final: 0.8203 (tmm) REVERT: H 377 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8384 (mm) REVERT: H 412 LEU cc_start: 0.9321 (mm) cc_final: 0.9083 (mm) REVERT: H 480 LYS cc_start: 0.9222 (mttt) cc_final: 0.8765 (mmmm) REVERT: I 123 MET cc_start: 0.7281 (mmp) cc_final: 0.7051 (mmp) REVERT: I 138 MET cc_start: 0.8168 (ptm) cc_final: 0.7360 (ptp) REVERT: I 157 MET cc_start: 0.8431 (mmm) cc_final: 0.8156 (mmm) REVERT: I 239 LEU cc_start: 0.8734 (tp) cc_final: 0.8452 (mt) REVERT: I 477 MET cc_start: 0.4293 (mmt) cc_final: 0.2700 (mmt) REVERT: I 535 CYS cc_start: 0.6843 (t) cc_final: 0.6454 (t) REVERT: I 580 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.7882 (t80) REVERT: I 582 PHE cc_start: 0.5041 (m-80) cc_final: 0.4771 (m-80) REVERT: I 651 HIS cc_start: 0.7507 (OUTLIER) cc_final: 0.6693 (p-80) REVERT: I 673 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: I 711 ASP cc_start: 0.9103 (m-30) cc_final: 0.8588 (p0) REVERT: I 770 GLU cc_start: 0.6386 (mt-10) cc_final: 0.6106 (tt0) REVERT: J 43 GLU cc_start: 0.9070 (pm20) cc_final: 0.8680 (pm20) outliers start: 65 outliers final: 40 residues processed: 243 average time/residue: 0.2605 time to fit residues: 99.8680 Evaluate side-chains 238 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 193 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 51 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 425 ASN Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 651 HIS Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain I residue 696 ASP Chi-restraints excluded: chain J residue 45 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 186 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 HIS D 155 GLN H 61 GLN ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17260 Z= 0.228 Angle : 0.658 12.060 23423 Z= 0.328 Chirality : 0.043 0.214 2688 Planarity : 0.005 0.088 3011 Dihedral : 5.556 56.194 2338 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.81 % Favored : 91.09 % Rotamer: Outliers : 3.65 % Allowed : 21.02 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -2.66 (0.17), residues: 2167 helix: -0.55 (0.17), residues: 869 sheet: -1.83 (0.25), residues: 368 loop : -2.93 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 9 HIS 0.015 0.001 HIS A 581 PHE 0.019 0.001 PHE I 721 TYR 0.018 0.001 TYR H 304 ARG 0.004 0.000 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 200 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 HIS cc_start: 0.7816 (OUTLIER) cc_final: 0.6860 (p-80) REVERT: A 584 MET cc_start: 0.8271 (ppp) cc_final: 0.7312 (ppp) REVERT: D 173 MET cc_start: 0.8969 (mmm) cc_final: 0.8548 (mmm) REVERT: D 203 GLU cc_start: 0.8484 (mp0) cc_final: 0.8051 (mp0) REVERT: D 260 ARG cc_start: 0.8812 (mtt180) cc_final: 0.8558 (mtt-85) REVERT: D 337 MET cc_start: 0.8765 (tpp) cc_final: 0.7932 (tpp) REVERT: D 339 GLU cc_start: 0.8595 (mp0) cc_final: 0.8005 (mp0) REVERT: D 361 TYR cc_start: 0.8281 (t80) cc_final: 0.8050 (t80) REVERT: H 50 GLU cc_start: 0.8911 (tp30) cc_final: 0.8690 (tp30) REVERT: H 186 PHE cc_start: 0.8618 (t80) cc_final: 0.8016 (t80) REVERT: H 190 PHE cc_start: 0.9163 (m-80) cc_final: 0.8545 (m-80) REVERT: H 295 MET cc_start: 0.9335 (mmt) cc_final: 0.8871 (mpp) REVERT: H 377 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8450 (mm) REVERT: H 412 LEU cc_start: 0.9310 (mm) cc_final: 0.9052 (mm) REVERT: H 480 LYS cc_start: 0.9182 (mttt) cc_final: 0.8693 (mmmm) REVERT: I 123 MET cc_start: 0.7265 (mmp) cc_final: 0.7049 (mmp) REVERT: I 239 LEU cc_start: 0.8746 (tp) cc_final: 0.8488 (mt) REVERT: I 477 MET cc_start: 0.4258 (mmt) cc_final: 0.2659 (mmt) REVERT: I 481 LEU cc_start: 0.5650 (OUTLIER) cc_final: 0.4938 (pt) REVERT: I 580 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7946 (t80) REVERT: I 651 HIS cc_start: 0.7365 (OUTLIER) cc_final: 0.6560 (p-80) REVERT: I 673 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: I 711 ASP cc_start: 0.9063 (m-30) cc_final: 0.8526 (p0) REVERT: I 770 GLU cc_start: 0.6249 (mt-10) cc_final: 0.5980 (tt0) REVERT: J 43 GLU cc_start: 0.9041 (pm20) cc_final: 0.8599 (pm20) outliers start: 65 outliers final: 44 residues processed: 250 average time/residue: 0.2458 time to fit residues: 97.6193 Evaluate side-chains 241 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 191 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 51 CYS Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 425 ASN Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 546 HIS Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 620 LEU Chi-restraints excluded: chain I residue 651 HIS Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain I residue 696 ASP Chi-restraints excluded: chain J residue 45 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 208 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 HIS ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17260 Z= 0.345 Angle : 0.719 11.979 23423 Z= 0.362 Chirality : 0.045 0.209 2688 Planarity : 0.005 0.087 3011 Dihedral : 5.708 55.643 2338 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.34 % Favored : 89.57 % Rotamer: Outliers : 4.27 % Allowed : 22.03 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.10 % 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: -2.68 (0.17), residues: 2167 helix: -0.51 (0.17), residues: 875 sheet: -1.92 (0.25), residues: 385 loop : -2.97 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 9 HIS 0.018 0.001 HIS A 581 PHE 0.025 0.002 PHE H 238 TYR 0.021 0.002 TYR H 304 ARG 0.005 0.000 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 195 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.7345 (mmm-85) REVERT: A 581 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.6891 (p-80) REVERT: A 584 MET cc_start: 0.8285 (ppp) cc_final: 0.7382 (ppp) REVERT: D 136 GLU cc_start: 0.8472 (pm20) cc_final: 0.8055 (pm20) REVERT: D 173 MET cc_start: 0.9156 (mmm) cc_final: 0.8749 (mmm) REVERT: D 203 GLU cc_start: 0.8453 (mp0) cc_final: 0.7970 (mp0) REVERT: D 260 ARG cc_start: 0.8878 (mtt180) cc_final: 0.8641 (mtt-85) REVERT: D 337 MET cc_start: 0.8808 (tpp) cc_final: 0.7991 (tpp) REVERT: D 339 GLU cc_start: 0.8658 (mp0) cc_final: 0.8018 (mp0) REVERT: H 50 GLU cc_start: 0.8880 (tp30) cc_final: 0.8659 (tp30) REVERT: H 190 PHE cc_start: 0.9234 (m-80) cc_final: 0.8897 (m-80) REVERT: H 230 MET cc_start: 0.7220 (ttm) cc_final: 0.6678 (ttm) REVERT: H 295 MET cc_start: 0.9289 (mmt) cc_final: 0.8809 (mpp) REVERT: H 377 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8472 (mm) REVERT: H 412 LEU cc_start: 0.9411 (mm) cc_final: 0.8782 (mm) REVERT: H 453 HIS cc_start: 0.8131 (m-70) cc_final: 0.7893 (m-70) REVERT: H 480 LYS cc_start: 0.9242 (mttt) cc_final: 0.8731 (mmmm) REVERT: I 239 LEU cc_start: 0.8730 (tp) cc_final: 0.8499 (mt) REVERT: I 477 MET cc_start: 0.4374 (mmt) cc_final: 0.2710 (mmt) REVERT: I 481 LEU cc_start: 0.5762 (OUTLIER) cc_final: 0.4979 (pt) REVERT: I 580 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7906 (t80) REVERT: I 635 SER cc_start: 0.7367 (OUTLIER) cc_final: 0.7061 (p) REVERT: I 651 HIS cc_start: 0.7404 (OUTLIER) cc_final: 0.6627 (p-80) REVERT: I 673 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8446 (m-80) REVERT: I 770 GLU cc_start: 0.6342 (mt-10) cc_final: 0.6062 (tt0) outliers start: 76 outliers final: 54 residues processed: 252 average time/residue: 0.2519 time to fit residues: 99.9041 Evaluate side-chains 249 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 188 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 51 CYS Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 425 ASN Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 289 CYS Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 546 HIS Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 620 LEU Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 640 ILE Chi-restraints excluded: chain I residue 651 HIS Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain I residue 696 ASP Chi-restraints excluded: chain J residue 45 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 chunk 117 optimal weight: 0.1980 chunk 175 optimal weight: 0.0670 chunk 116 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 129 optimal weight: 0.0470 chunk 126 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 HIS ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17260 Z= 0.157 Angle : 0.654 12.161 23423 Z= 0.320 Chirality : 0.043 0.218 2688 Planarity : 0.004 0.081 3011 Dihedral : 5.257 54.129 2338 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.03 % Favored : 91.88 % Rotamer: Outliers : 2.98 % Allowed : 23.89 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -2.20 (0.18), residues: 2167 helix: 0.01 (0.18), residues: 865 sheet: -1.65 (0.26), residues: 363 loop : -2.82 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 741 HIS 0.011 0.001 HIS A 581 PHE 0.019 0.001 PHE H 238 TYR 0.021 0.001 TYR D 361 ARG 0.003 0.000 ARG I 669 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 212 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.9080 (ttp-170) cc_final: 0.8385 (mmt180) REVERT: A 581 HIS cc_start: 0.7521 (OUTLIER) cc_final: 0.6758 (p-80) REVERT: A 584 MET cc_start: 0.8192 (ppp) cc_final: 0.7245 (ppp) REVERT: D 173 MET cc_start: 0.9125 (mmm) cc_final: 0.8726 (mmm) REVERT: D 203 GLU cc_start: 0.8468 (mp0) cc_final: 0.8031 (mp0) REVERT: D 260 ARG cc_start: 0.8802 (mtt180) cc_final: 0.8535 (mtt-85) REVERT: D 275 ASN cc_start: 0.8286 (m-40) cc_final: 0.8051 (m110) REVERT: D 337 MET cc_start: 0.8618 (tpp) cc_final: 0.7926 (tpp) REVERT: D 339 GLU cc_start: 0.8527 (mp0) cc_final: 0.7991 (mp0) REVERT: H 50 GLU cc_start: 0.8921 (tp30) cc_final: 0.8639 (tp30) REVERT: H 190 PHE cc_start: 0.9020 (m-80) cc_final: 0.8751 (m-80) REVERT: H 230 MET cc_start: 0.7218 (ttm) cc_final: 0.6987 (ttm) REVERT: H 295 MET cc_start: 0.9322 (mmt) cc_final: 0.8915 (mpp) REVERT: H 377 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8455 (mm) REVERT: H 412 LEU cc_start: 0.9290 (mm) cc_final: 0.8668 (mm) REVERT: H 479 GLN cc_start: 0.8651 (tp40) cc_final: 0.8185 (tt0) REVERT: H 480 LYS cc_start: 0.9170 (mttt) cc_final: 0.8686 (mmmm) REVERT: I 239 LEU cc_start: 0.8895 (tp) cc_final: 0.8678 (mt) REVERT: I 477 MET cc_start: 0.4163 (mmt) cc_final: 0.2604 (mmt) REVERT: I 481 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.4729 (pt) REVERT: I 580 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7949 (t80) REVERT: I 635 SER cc_start: 0.7126 (OUTLIER) cc_final: 0.6779 (p) REVERT: I 651 HIS cc_start: 0.7301 (OUTLIER) cc_final: 0.6489 (p-80) REVERT: I 673 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8401 (m-80) REVERT: I 770 GLU cc_start: 0.6174 (mt-10) cc_final: 0.5927 (tt0) REVERT: J 43 GLU cc_start: 0.9007 (pm20) cc_final: 0.8799 (pm20) outliers start: 53 outliers final: 33 residues processed: 251 average time/residue: 0.2539 time to fit residues: 99.9499 Evaluate side-chains 237 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 546 HIS Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 599 TYR Chi-restraints excluded: chain I residue 620 LEU Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 651 HIS Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain I residue 696 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 0.0270 chunk 131 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 overall best weight: 1.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 621 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17260 Z= 0.227 Angle : 0.685 11.981 23423 Z= 0.337 Chirality : 0.044 0.215 2688 Planarity : 0.005 0.081 3011 Dihedral : 5.257 53.086 2338 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.77 % Favored : 91.14 % Rotamer: Outliers : 3.04 % Allowed : 24.34 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -2.10 (0.18), residues: 2167 helix: 0.05 (0.18), residues: 877 sheet: -1.61 (0.26), residues: 372 loop : -2.76 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 135 HIS 0.011 0.001 HIS A 581 PHE 0.034 0.002 PHE H 271 TYR 0.032 0.001 TYR D 361 ARG 0.003 0.000 ARG I 669 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 198 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.9096 (ttp-170) cc_final: 0.8405 (mmt180) REVERT: A 182 MET cc_start: 0.4138 (tmm) cc_final: 0.3785 (ppp) REVERT: A 581 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.7212 (p90) REVERT: A 584 MET cc_start: 0.8150 (ppp) cc_final: 0.7207 (ppp) REVERT: D 173 MET cc_start: 0.9155 (mmm) cc_final: 0.8727 (mmm) REVERT: D 203 GLU cc_start: 0.8400 (mp0) cc_final: 0.7935 (mp0) REVERT: D 260 ARG cc_start: 0.8828 (mtt180) cc_final: 0.8585 (mtt-85) REVERT: D 337 MET cc_start: 0.8675 (tpp) cc_final: 0.7947 (tpp) REVERT: D 339 GLU cc_start: 0.8556 (mp0) cc_final: 0.7915 (mp0) REVERT: H 50 GLU cc_start: 0.8921 (tp30) cc_final: 0.8647 (tp30) REVERT: H 190 PHE cc_start: 0.9088 (m-80) cc_final: 0.8807 (m-80) REVERT: H 295 MET cc_start: 0.9355 (mmt) cc_final: 0.8935 (mpp) REVERT: H 377 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8446 (mm) REVERT: H 412 LEU cc_start: 0.9351 (mm) cc_final: 0.8733 (mm) REVERT: H 479 GLN cc_start: 0.8728 (tp40) cc_final: 0.8250 (tt0) REVERT: H 480 LYS cc_start: 0.9200 (mttt) cc_final: 0.8747 (mmmm) REVERT: I 239 LEU cc_start: 0.8900 (tp) cc_final: 0.8670 (mt) REVERT: I 477 MET cc_start: 0.4376 (mmt) cc_final: 0.2802 (mmt) REVERT: I 481 LEU cc_start: 0.5598 (OUTLIER) cc_final: 0.4891 (pt) REVERT: I 501 GLU cc_start: 0.8620 (pp20) cc_final: 0.8258 (pp20) REVERT: I 635 SER cc_start: 0.7213 (OUTLIER) cc_final: 0.6875 (p) REVERT: I 651 HIS cc_start: 0.7291 (OUTLIER) cc_final: 0.6452 (p-80) REVERT: I 673 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8384 (m-80) REVERT: I 770 GLU cc_start: 0.6256 (mt-10) cc_final: 0.5997 (tt0) outliers start: 54 outliers final: 37 residues processed: 238 average time/residue: 0.2518 time to fit residues: 94.3107 Evaluate side-chains 237 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 194 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 546 HIS Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 599 TYR Chi-restraints excluded: chain I residue 620 LEU Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 651 HIS Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain I residue 696 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 193 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 174 optimal weight: 0.0980 chunk 182 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 126 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 313 HIS ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17260 Z= 0.162 Angle : 0.668 12.491 23423 Z= 0.323 Chirality : 0.043 0.218 2688 Planarity : 0.004 0.077 3011 Dihedral : 4.997 52.259 2338 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.03 % Favored : 91.88 % Rotamer: Outliers : 2.36 % Allowed : 24.96 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -1.82 (0.18), residues: 2167 helix: 0.27 (0.18), residues: 875 sheet: -1.36 (0.27), residues: 375 loop : -2.65 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 741 HIS 0.003 0.001 HIS H 192 PHE 0.021 0.001 PHE H 271 TYR 0.017 0.001 TYR I 703 ARG 0.004 0.000 ARG I 528 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 219 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.9080 (ttp-170) cc_final: 0.8391 (mmt180) REVERT: A 182 MET cc_start: 0.4282 (tmm) cc_final: 0.3898 (ppp) REVERT: A 584 MET cc_start: 0.8186 (ppp) cc_final: 0.7269 (ppp) REVERT: D 173 MET cc_start: 0.9094 (mmm) cc_final: 0.8704 (mmm) REVERT: D 200 GLU cc_start: 0.8138 (pm20) cc_final: 0.7853 (pm20) REVERT: D 203 GLU cc_start: 0.8438 (mp0) cc_final: 0.8047 (mp0) REVERT: D 260 ARG cc_start: 0.8769 (mtt180) cc_final: 0.8514 (mtt-85) REVERT: D 275 ASN cc_start: 0.8276 (m-40) cc_final: 0.8056 (m110) REVERT: D 339 GLU cc_start: 0.8510 (mp0) cc_final: 0.8211 (mp0) REVERT: H 5 MET cc_start: 0.8014 (pmm) cc_final: 0.7784 (ppp) REVERT: H 50 GLU cc_start: 0.8925 (tp30) cc_final: 0.8659 (tp30) REVERT: H 190 PHE cc_start: 0.8987 (m-80) cc_final: 0.8713 (m-80) REVERT: H 236 LYS cc_start: 0.9303 (tttt) cc_final: 0.9046 (tmtt) REVERT: H 295 MET cc_start: 0.9314 (mmt) cc_final: 0.8960 (mpp) REVERT: H 377 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8431 (mm) REVERT: H 412 LEU cc_start: 0.9278 (mm) cc_final: 0.8673 (mm) REVERT: H 479 GLN cc_start: 0.8610 (tp40) cc_final: 0.8223 (tt0) REVERT: H 480 LYS cc_start: 0.9137 (mttt) cc_final: 0.8755 (mmmt) REVERT: I 477 MET cc_start: 0.4325 (mmt) cc_final: 0.2827 (mmt) REVERT: I 481 LEU cc_start: 0.5343 (OUTLIER) cc_final: 0.4643 (pt) REVERT: I 501 GLU cc_start: 0.8620 (pp20) cc_final: 0.8353 (pp20) REVERT: I 635 SER cc_start: 0.7044 (OUTLIER) cc_final: 0.6696 (p) REVERT: I 673 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: I 768 TRP cc_start: 0.7102 (t60) cc_final: 0.6883 (t60) REVERT: I 770 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5908 (tt0) outliers start: 42 outliers final: 32 residues processed: 248 average time/residue: 0.2524 time to fit residues: 97.8838 Evaluate side-chains 234 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 198 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 546 HIS Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 599 TYR Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 640 ILE Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain I residue 696 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 141 optimal weight: 0.0040 chunk 214 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 131 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 395 HIS H 420 HIS ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17260 Z= 0.211 Angle : 0.687 11.697 23423 Z= 0.337 Chirality : 0.044 0.228 2688 Planarity : 0.004 0.078 3011 Dihedral : 5.036 51.624 2338 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.12 % Favored : 91.79 % Rotamer: Outliers : 2.30 % Allowed : 25.58 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.18), residues: 2167 helix: 0.33 (0.18), residues: 877 sheet: -1.33 (0.27), residues: 366 loop : -2.68 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 139 HIS 0.004 0.001 HIS H 192 PHE 0.020 0.001 PHE H 271 TYR 0.017 0.001 TYR H 304 ARG 0.008 0.000 ARG I 679 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 197 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.9061 (ttp-170) cc_final: 0.8397 (mmt180) REVERT: A 182 MET cc_start: 0.4316 (tmm) cc_final: 0.3964 (ppp) REVERT: A 584 MET cc_start: 0.8202 (ppp) cc_final: 0.7290 (ppp) REVERT: D 173 MET cc_start: 0.9159 (mmm) cc_final: 0.8729 (mmm) REVERT: D 203 GLU cc_start: 0.8419 (mp0) cc_final: 0.7966 (mp0) REVERT: D 260 ARG cc_start: 0.8799 (mtt180) cc_final: 0.8539 (mtt-85) REVERT: D 275 ASN cc_start: 0.8210 (m-40) cc_final: 0.7934 (m110) REVERT: D 337 MET cc_start: 0.8680 (tpp) cc_final: 0.8029 (tpp) REVERT: D 339 GLU cc_start: 0.8518 (mp0) cc_final: 0.7983 (mp0) REVERT: H 50 GLU cc_start: 0.8920 (tp30) cc_final: 0.8664 (tp30) REVERT: H 190 PHE cc_start: 0.9047 (m-80) cc_final: 0.8767 (m-80) REVERT: H 236 LYS cc_start: 0.9302 (tttt) cc_final: 0.9022 (tmtt) REVERT: H 295 MET cc_start: 0.9309 (mmt) cc_final: 0.8961 (mpp) REVERT: H 377 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8435 (mm) REVERT: H 383 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7497 (tp30) REVERT: H 412 LEU cc_start: 0.9318 (mm) cc_final: 0.8878 (mm) REVERT: H 432 MET cc_start: 0.7940 (tpt) cc_final: 0.7641 (tpp) REVERT: H 479 GLN cc_start: 0.8698 (tp40) cc_final: 0.8238 (tt0) REVERT: H 480 LYS cc_start: 0.9141 (mttt) cc_final: 0.8687 (mmmm) REVERT: I 162 MET cc_start: 0.8099 (mmp) cc_final: 0.7664 (mmp) REVERT: I 477 MET cc_start: 0.4317 (mmt) cc_final: 0.2757 (mmt) REVERT: I 481 LEU cc_start: 0.5599 (OUTLIER) cc_final: 0.4949 (pt) REVERT: I 501 GLU cc_start: 0.8611 (pp20) cc_final: 0.8266 (pp20) REVERT: I 635 SER cc_start: 0.7119 (OUTLIER) cc_final: 0.6791 (p) REVERT: I 673 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.8294 (m-80) REVERT: I 768 TRP cc_start: 0.7125 (t60) cc_final: 0.6882 (t60) REVERT: I 770 GLU cc_start: 0.6232 (mt-10) cc_final: 0.5968 (tt0) REVERT: J 69 MET cc_start: 0.7805 (ttp) cc_final: 0.7065 (tmm) outliers start: 41 outliers final: 35 residues processed: 226 average time/residue: 0.2607 time to fit residues: 92.6885 Evaluate side-chains 231 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 414 LEU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 546 HIS Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 599 TYR Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 640 ILE Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain I residue 696 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 chunk 157 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.105977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.075507 restraints weight = 55241.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.077984 restraints weight = 30023.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.079593 restraints weight = 20882.841| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17260 Z= 0.255 Angle : 0.710 11.567 23423 Z= 0.348 Chirality : 0.045 0.250 2688 Planarity : 0.005 0.081 3011 Dihedral : 5.190 52.295 2338 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.77 % Favored : 91.14 % Rotamer: Outliers : 2.70 % Allowed : 25.18 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.18), residues: 2167 helix: 0.27 (0.18), residues: 878 sheet: -1.38 (0.26), residues: 379 loop : -2.70 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 237 HIS 0.005 0.001 HIS H 192 PHE 0.019 0.002 PHE H 238 TYR 0.020 0.001 TYR H 304 ARG 0.010 0.000 ARG I 679 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3270.76 seconds wall clock time: 59 minutes 25.77 seconds (3565.77 seconds total)