Starting phenix.real_space_refine on Mon Nov 18 02:30:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdb_37460/11_2024/8wdb_37460.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdb_37460/11_2024/8wdb_37460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdb_37460/11_2024/8wdb_37460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdb_37460/11_2024/8wdb_37460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdb_37460/11_2024/8wdb_37460.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdb_37460/11_2024/8wdb_37460.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3598 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 7847 2.51 5 N 2198 2.21 5 O 2242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12322 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3892 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 25, 'TRANS': 487} Chain breaks: 1 Chain: "B" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2302 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 292} Chain: "C" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2102 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 13, 'TRANS': 267} Chain: "A" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3962 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 41, 'TRANS': 475} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 8.06, per 1000 atoms: 0.65 Number of scatterers: 12322 At special positions: 0 Unit cell: (83.64, 87.74, 159.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 P 6 15.00 Mg 2 11.99 O 2242 8.00 N 2198 7.00 C 7847 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: 3.30 Conformation dependent library (CDL) restraints added in 1.8 seconds 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 10 sheets defined 54.2% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'D' and resid 47 through 57 removed outlier: 3.511A pdb=" N ALA D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 removed outlier: 4.519A pdb=" N GLY D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 118 removed outlier: 3.757A pdb=" N ALA D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 139 removed outlier: 3.991A pdb=" N VAL D 132 " --> pdb=" O ARG D 128 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU D 133 " --> pdb=" O ARG D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 148 through 149 No H-bonds generated for 'chain 'D' and resid 148 through 149' Processing helix chain 'D' and resid 150 through 154 Processing helix chain 'D' and resid 155 through 168 removed outlier: 3.794A pdb=" N GLN D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 200 Processing helix chain 'D' and resid 213 through 221 removed outlier: 3.899A pdb=" N ALA D 217 " --> pdb=" O ASP D 213 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 329 through 338 removed outlier: 3.529A pdb=" N LEU D 333 " --> pdb=" O GLY D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 369 removed outlier: 4.565A pdb=" N ALA D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 399 Proline residue: D 395 - end of helix Processing helix chain 'D' and resid 404 through 418 Processing helix chain 'D' and resid 421 through 425 removed outlier: 3.650A pdb=" N ILE D 424 " --> pdb=" O PRO D 421 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 425 " --> pdb=" O SER D 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 421 through 425' Processing helix chain 'D' and resid 428 through 432 removed outlier: 3.532A pdb=" N LEU D 432 " --> pdb=" O PRO D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 447 removed outlier: 3.588A pdb=" N ARG D 437 " --> pdb=" O SER D 433 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN D 438 " --> pdb=" O GLY D 434 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG D 439 " --> pdb=" O GLY D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 481 removed outlier: 4.056A pdb=" N GLN D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 499 removed outlier: 3.590A pdb=" N ILE D 495 " --> pdb=" O ASP D 491 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN D 497 " --> pdb=" O ALA D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 525 through 533 Processing helix chain 'B' and resid 2 through 29 removed outlier: 4.361A pdb=" N VAL B 13 " --> pdb=" O VAL B 9 " (cutoff:3.500A) Proline residue: B 14 - end of helix Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 45 through 56 removed outlier: 3.677A pdb=" N ALA B 50 " --> pdb=" O PRO B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 72 removed outlier: 3.696A pdb=" N GLY B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.867A pdb=" N GLY B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 85' Processing helix chain 'B' and resid 86 through 123 removed outlier: 3.672A pdb=" N VAL B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 126 through 142 Processing helix chain 'B' and resid 143 through 158 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.964A pdb=" N VAL B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 removed outlier: 3.788A pdb=" N ARG B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 209 " --> pdb=" O ASP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 230 through 245 removed outlier: 4.277A pdb=" N GLY B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 259 through 271 removed outlier: 3.978A pdb=" N VAL B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 302 removed outlier: 3.528A pdb=" N VAL B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 17 removed outlier: 4.009A pdb=" N ARG C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 37 Processing helix chain 'C' and resid 38 through 41 Processing helix chain 'C' and resid 50 through 54 removed outlier: 3.828A pdb=" N SER C 54 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 80 through 110 Processing helix chain 'C' and resid 112 through 127 removed outlier: 3.646A pdb=" N GLY C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 127 " --> pdb=" O VAL C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 137 removed outlier: 3.952A pdb=" N ALA C 132 " --> pdb=" O PRO C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 172 removed outlier: 3.635A pdb=" N VAL C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) Proline residue: C 158 - end of helix removed outlier: 3.764A pdb=" N GLU C 170 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 184 removed outlier: 3.731A pdb=" N LEU C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 196 Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 200 through 224 removed outlier: 4.545A pdb=" N GLY C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA C 219 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 244 through 247 removed outlier: 4.347A pdb=" N ARG C 247 " --> pdb=" O THR C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 244 through 247' Processing helix chain 'C' and resid 253 through 276 removed outlier: 3.583A pdb=" N ALA C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 259 " --> pdb=" O TYR C 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.866A pdb=" N THR A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 64 removed outlier: 4.325A pdb=" N ILE A 59 " --> pdb=" O ASN A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 122 removed outlier: 3.977A pdb=" N PHE A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 138 through 144 removed outlier: 3.714A pdb=" N VAL A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.765A pdb=" N ARG A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 180 " --> pdb=" O PHE A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 175 through 180' Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.776A pdb=" N ALA A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.669A pdb=" N LEU A 276 " --> pdb=" O PRO A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 309 through 321 removed outlier: 3.901A pdb=" N ARG A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.568A pdb=" N GLN A 330 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.555A pdb=" N VAL A 360 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 362 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 377 Processing helix chain 'A' and resid 395 through 410 Processing helix chain 'A' and resid 424 through 431 removed outlier: 3.603A pdb=" N GLN A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 452 Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.702A pdb=" N THR A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 482 removed outlier: 3.550A pdb=" N ALA A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 504 removed outlier: 3.573A pdb=" N HIS A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU A 491 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 removed outlier: 3.582A pdb=" N ASN A 537 " --> pdb=" O ASP A 534 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 538 " --> pdb=" O TYR A 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 534 through 538' Processing sheet with id=AA1, first strand: chain 'D' and resid 25 through 32 removed outlier: 6.894A pdb=" N CYS D 26 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU D 15 " --> pdb=" O CYS D 26 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL D 28 " --> pdb=" O GLY D 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 25 through 32 removed outlier: 6.894A pdb=" N CYS D 26 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU D 15 " --> pdb=" O CYS D 26 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL D 28 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG D 69 " --> pdb=" O GLU D 12 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE D 72 " --> pdb=" O ARG D 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 94 through 96 removed outlier: 6.423A pdb=" N VAL D 38 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 234 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG D 228 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N VAL D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 301 through 315 removed outlier: 6.539A pdb=" N LYS D 289 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP D 308 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU D 287 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL D 310 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER D 285 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE D 312 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL D 283 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU D 314 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU D 287 " --> pdb=" O SER D 345 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER D 345 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 371 through 374 removed outlier: 6.702A pdb=" N GLN D 372 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ASP D 456 " --> pdb=" O GLN D 372 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL D 374 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 488 " --> pdb=" O CYS D 455 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 512 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG D 506 " --> pdb=" O VAL D 510 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N VAL D 510 " --> pdb=" O ARG D 506 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.501A pdb=" N VAL A 35 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLU A 248 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 37 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.501A pdb=" N VAL A 35 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLU A 248 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 37 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA9, first strand: chain 'A' and resid 81 through 85 removed outlier: 6.734A pdb=" N THR A 95 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE A 84 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ARG A 93 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 337 through 339 removed outlier: 7.523A pdb=" N GLN A 296 " --> pdb=" O PRO A 508 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TRP A 510 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE A 294 " --> pdb=" O TRP A 510 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR A 512 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN A 390 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR A 385 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ALA A 417 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE A 387 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N GLN A 419 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TYR A 389 " --> pdb=" O GLN A 419 " (cutoff:3.500A) 591 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2001 1.28 - 1.41: 3170 1.41 - 1.55: 7354 1.55 - 1.68: 14 1.68 - 1.81: 49 Bond restraints: 12588 Sorted by residual: bond pdb=" C4 ATP D 602 " pdb=" C5 ATP D 602 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.60e+01 bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.58e+01 bond pdb=" C GLN A 130 " pdb=" O GLN A 130 " ideal model delta sigma weight residual 1.236 1.150 0.086 1.18e-02 7.18e+03 5.35e+01 bond pdb=" C5 ATP D 601 " pdb=" C6 ATP D 601 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.20e+01 bond pdb=" C5 ATP D 602 " pdb=" C6 ATP D 602 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.10e+01 ... (remaining 12583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 16975 3.11 - 6.21: 186 6.21 - 9.32: 27 9.32 - 12.42: 5 12.42 - 15.53: 4 Bond angle restraints: 17197 Sorted by residual: angle pdb=" PA ATP D 601 " pdb=" O3A ATP D 601 " pdb=" PB ATP D 601 " ideal model delta sigma weight residual 136.83 121.30 15.53 1.00e+00 1.00e+00 2.41e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 124.51 15.36 1.00e+00 1.00e+00 2.36e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 125.35 14.52 1.00e+00 1.00e+00 2.11e+02 angle pdb=" PA ATP D 602 " pdb=" O3A ATP D 602 " pdb=" PB ATP D 602 " ideal model delta sigma weight residual 136.83 124.48 12.35 1.00e+00 1.00e+00 1.53e+02 angle pdb=" C5 ATP D 601 " pdb=" C4 ATP D 601 " pdb=" N3 ATP D 601 " ideal model delta sigma weight residual 126.80 118.79 8.01 1.00e+00 1.00e+00 6.42e+01 ... (remaining 17192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 6868 17.82 - 35.63: 501 35.63 - 53.45: 92 53.45 - 71.26: 18 71.26 - 89.08: 14 Dihedral angle restraints: 7493 sinusoidal: 2889 harmonic: 4604 Sorted by residual: dihedral pdb=" CA ALA D 458 " pdb=" C ALA D 458 " pdb=" N VAL D 459 " pdb=" CA VAL D 459 " ideal model delta harmonic sigma weight residual 180.00 151.57 28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA TRP D 108 " pdb=" C TRP D 108 " pdb=" N LYS D 109 " pdb=" CA LYS D 109 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA TYR A 250 " pdb=" C TYR A 250 " pdb=" N ALA A 251 " pdb=" CA ALA A 251 " ideal model delta harmonic sigma weight residual 180.00 153.58 26.42 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 7490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1879 0.099 - 0.199: 123 0.199 - 0.298: 0 0.298 - 0.398: 0 0.398 - 0.497: 2 Chirality restraints: 2004 Sorted by residual: chirality pdb=" CA ALA D 360 " pdb=" N ALA D 360 " pdb=" C ALA D 360 " pdb=" CB ALA D 360 " both_signs ideal model delta sigma weight residual False 2.48 1.99 0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" CA PHE C 7 " pdb=" N PHE C 7 " pdb=" C PHE C 7 " pdb=" CB PHE C 7 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA ARG A 443 " pdb=" N ARG A 443 " pdb=" C ARG A 443 " pdb=" CB ARG A 443 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.82e-01 ... (remaining 2001 not shown) Planarity restraints: 2229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 63 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C LEU B 63 " -0.068 2.00e-02 2.50e+03 pdb=" O LEU B 63 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL B 64 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 4 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C HIS C 4 " -0.057 2.00e-02 2.50e+03 pdb=" O HIS C 4 " 0.022 2.00e-02 2.50e+03 pdb=" N THR C 5 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 192 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LEU C 192 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU C 192 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG C 193 " 0.019 2.00e-02 2.50e+03 ... (remaining 2226 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 90 2.58 - 3.16: 10041 3.16 - 3.74: 17715 3.74 - 4.32: 26300 4.32 - 4.90: 44534 Nonbonded interactions: 98680 Sorted by model distance: nonbonded pdb=" O HIS C 4 " pdb=" O THR C 5 " model vdw 2.006 3.040 nonbonded pdb=" O2B ATP D 601 " pdb="MG MG D 603 " model vdw 2.042 2.170 nonbonded pdb=" N ASP B 41 " pdb=" OD1 ASP B 41 " model vdw 2.081 3.120 nonbonded pdb=" OG SER D 49 " pdb="MG MG D 603 " model vdw 2.097 2.170 nonbonded pdb=" OG1 THR B 235 " pdb=" OH TYR B 298 " model vdw 2.161 3.040 ... (remaining 98675 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.020 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 12588 Z= 0.496 Angle : 0.890 15.528 17197 Z= 0.557 Chirality : 0.051 0.497 2004 Planarity : 0.006 0.051 2229 Dihedral : 13.651 89.081 4547 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.89 % Favored : 91.67 % Rotamer: Outliers : 0.55 % Allowed : 4.10 % Favored : 95.34 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.18), residues: 1609 helix: -1.40 (0.17), residues: 763 sheet: -1.57 (0.39), residues: 154 loop : -2.62 (0.20), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 8 HIS 0.007 0.001 HIS C 71 PHE 0.020 0.002 PHE B 149 TYR 0.016 0.002 TYR C 223 ARG 0.008 0.000 ARG D 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: C 270 MET cc_start: 0.8299 (tpt) cc_final: 0.8082 (tpt) REVERT: A 175 ASP cc_start: 0.7835 (t0) cc_final: 0.7467 (t0) REVERT: A 400 ASP cc_start: 0.8134 (m-30) cc_final: 0.7890 (m-30) outliers start: 7 outliers final: 4 residues processed: 133 average time/residue: 1.6235 time to fit residues: 231.2422 Evaluate side-chains 97 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 8 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 0.4980 chunk 145 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 ASN D 153 GLN D 160 GLN D 189 GLN D 219 GLN D 243 GLN D 247 HIS D 372 GLN D 417 GLN D 438 GLN B 65 GLN B 271 GLN C 69 GLN C 71 HIS C 159 GLN A 182 HIS A 242 ASN A 306 HIS A 331 GLN A 408 ASN A 428 GLN A 497 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 12588 Z= 0.198 Angle : 0.617 9.204 17197 Z= 0.325 Chirality : 0.043 0.169 2004 Planarity : 0.005 0.039 2229 Dihedral : 7.573 88.112 1859 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.59 % Favored : 93.23 % Rotamer: Outliers : 2.05 % Allowed : 8.13 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.20), residues: 1609 helix: -0.13 (0.19), residues: 774 sheet: -1.04 (0.39), residues: 153 loop : -2.02 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 8 HIS 0.005 0.001 HIS B 224 PHE 0.014 0.001 PHE C 155 TYR 0.010 0.001 TYR C 109 ARG 0.006 0.000 ARG D 522 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: D 86 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7252 (ttp-170) REVERT: D 246 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7776 (mp10) REVERT: C 1 MET cc_start: 0.6002 (ptp) cc_final: 0.3842 (pp-130) REVERT: A 218 PRO cc_start: 0.8329 (Cg_exo) cc_final: 0.8127 (Cg_endo) REVERT: A 221 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: A 366 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: A 400 ASP cc_start: 0.8001 (m-30) cc_final: 0.7759 (m-30) outliers start: 26 outliers final: 8 residues processed: 134 average time/residue: 1.2903 time to fit residues: 188.5146 Evaluate side-chains 108 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 8 TRP Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 366 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 116 optimal weight: 0.0970 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 212 HIS D 243 GLN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS A 404 ASN A 497 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 12588 Z= 0.260 Angle : 0.614 9.096 17197 Z= 0.323 Chirality : 0.043 0.161 2004 Planarity : 0.005 0.040 2229 Dihedral : 7.076 84.458 1853 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.40 % Favored : 93.41 % Rotamer: Outliers : 2.60 % Allowed : 9.71 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.20), residues: 1609 helix: 0.34 (0.19), residues: 773 sheet: -0.82 (0.39), residues: 159 loop : -1.74 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 8 HIS 0.004 0.001 HIS B 224 PHE 0.016 0.001 PHE C 155 TYR 0.012 0.001 TYR C 223 ARG 0.005 0.000 ARG D 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: D 86 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7165 (ttp-170) REVERT: D 92 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7689 (mm-30) REVERT: B 80 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7559 (tpt170) REVERT: B 123 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6437 (ptm-80) REVERT: C 1 MET cc_start: 0.5974 (ptp) cc_final: 0.3863 (pp-130) REVERT: C 8 TRP cc_start: 0.7198 (OUTLIER) cc_final: 0.6282 (m100) REVERT: C 13 ARG cc_start: 0.6722 (mtt-85) cc_final: 0.6496 (mtt90) REVERT: A 218 PRO cc_start: 0.8212 (Cg_exo) cc_final: 0.8004 (Cg_endo) REVERT: A 221 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: A 366 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7831 (mt0) REVERT: A 400 ASP cc_start: 0.7993 (m-30) cc_final: 0.7768 (m-30) outliers start: 33 outliers final: 5 residues processed: 125 average time/residue: 1.3373 time to fit residues: 181.9615 Evaluate side-chains 104 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain C residue 8 TRP Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 366 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 12588 Z= 0.385 Angle : 0.670 8.844 17197 Z= 0.352 Chirality : 0.046 0.157 2004 Planarity : 0.005 0.048 2229 Dihedral : 7.220 81.844 1852 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.33 % Favored : 92.48 % Rotamer: Outliers : 2.84 % Allowed : 10.89 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1609 helix: 0.38 (0.19), residues: 768 sheet: -0.67 (0.40), residues: 159 loop : -1.73 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 8 HIS 0.005 0.001 HIS D 513 PHE 0.019 0.002 PHE C 155 TYR 0.015 0.002 TYR C 223 ARG 0.006 0.000 ARG D 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: D 86 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7144 (ttp-170) REVERT: B 123 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6660 (ptm-80) REVERT: C 1 MET cc_start: 0.5939 (ptp) cc_final: 0.3747 (pp-130) REVERT: C 8 TRP cc_start: 0.7292 (OUTLIER) cc_final: 0.6267 (m100) REVERT: C 13 ARG cc_start: 0.6808 (mtt-85) cc_final: 0.6600 (mtt90) REVERT: A 221 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: A 366 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: A 400 ASP cc_start: 0.8050 (m-30) cc_final: 0.7813 (m-30) REVERT: A 521 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7412 (mm-40) outliers start: 36 outliers final: 13 residues processed: 118 average time/residue: 1.3068 time to fit residues: 168.2325 Evaluate side-chains 110 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 8 TRP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 223 TYR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 521 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.134 12588 Z= 0.211 Angle : 0.587 9.252 17197 Z= 0.307 Chirality : 0.042 0.190 2004 Planarity : 0.004 0.040 2229 Dihedral : 6.878 84.903 1852 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.22 % Favored : 93.66 % Rotamer: Outliers : 2.37 % Allowed : 11.76 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.21), residues: 1609 helix: 0.73 (0.19), residues: 773 sheet: -0.46 (0.41), residues: 159 loop : -1.49 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 8 HIS 0.004 0.001 HIS B 224 PHE 0.014 0.001 PHE C 155 TYR 0.009 0.001 TYR C 223 ARG 0.007 0.000 ARG D 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 1.406 Fit side-chains revert: symmetry clash REVERT: D 86 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7100 (ttp-170) REVERT: B 123 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6715 (mtm180) REVERT: C 1 MET cc_start: 0.5801 (ptp) cc_final: 0.3767 (pp-130) REVERT: A 221 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: A 400 ASP cc_start: 0.7967 (m-30) cc_final: 0.7750 (m-30) REVERT: A 521 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7377 (mm-40) outliers start: 30 outliers final: 13 residues processed: 122 average time/residue: 1.3772 time to fit residues: 182.3654 Evaluate side-chains 106 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 521 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 128 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 219 GLN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN B 228 ASN A 161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 12588 Z= 0.377 Angle : 0.658 8.371 17197 Z= 0.345 Chirality : 0.046 0.166 2004 Planarity : 0.005 0.047 2229 Dihedral : 7.053 81.276 1850 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.90 % Favored : 92.91 % Rotamer: Outliers : 2.53 % Allowed : 12.79 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1609 helix: 0.64 (0.19), residues: 773 sheet: -0.45 (0.41), residues: 159 loop : -1.50 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 8 HIS 0.005 0.001 HIS C 71 PHE 0.018 0.002 PHE C 155 TYR 0.015 0.002 TYR C 223 ARG 0.004 0.000 ARG D 522 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: D 86 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7072 (ttp-170) REVERT: D 91 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6050 (mmm160) REVERT: B 123 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6752 (ptm-80) REVERT: A 221 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: A 400 ASP cc_start: 0.8045 (m-30) cc_final: 0.7803 (m-30) REVERT: A 521 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7228 (mm-40) outliers start: 32 outliers final: 15 residues processed: 113 average time/residue: 1.3910 time to fit residues: 170.9748 Evaluate side-chains 110 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 223 TYR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 521 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.148 12588 Z= 0.201 Angle : 0.576 7.742 17197 Z= 0.301 Chirality : 0.042 0.214 2004 Planarity : 0.004 0.039 2229 Dihedral : 6.709 86.851 1850 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.15 % Favored : 93.78 % Rotamer: Outliers : 1.74 % Allowed : 13.89 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1609 helix: 0.95 (0.19), residues: 773 sheet: -0.30 (0.42), residues: 159 loop : -1.34 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 8 HIS 0.004 0.001 HIS B 224 PHE 0.014 0.001 PHE C 155 TYR 0.008 0.001 TYR C 223 ARG 0.004 0.000 ARG D 522 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: D 73 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: C 1 MET cc_start: 0.5828 (ptp) cc_final: 0.3612 (pp-130) REVERT: A 221 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: A 400 ASP cc_start: 0.7935 (m-30) cc_final: 0.7706 (m-30) REVERT: A 521 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7431 (mm-40) outliers start: 22 outliers final: 10 residues processed: 111 average time/residue: 1.3252 time to fit residues: 160.3044 Evaluate side-chains 102 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 521 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.1980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 121 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.173 12588 Z= 0.208 Angle : 0.564 8.676 17197 Z= 0.294 Chirality : 0.042 0.239 2004 Planarity : 0.004 0.038 2229 Dihedral : 6.424 89.077 1850 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.34 % Allowed : 14.60 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1609 helix: 1.12 (0.19), residues: 777 sheet: -0.20 (0.41), residues: 169 loop : -1.22 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 8 HIS 0.004 0.001 HIS B 224 PHE 0.014 0.001 PHE C 155 TYR 0.008 0.001 TYR C 176 ARG 0.004 0.000 ARG D 316 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.460 Fit side-chains REVERT: D 73 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7365 (m-30) REVERT: D 86 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.6920 (ttp-170) REVERT: B 219 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7409 (ttt180) REVERT: C 1 MET cc_start: 0.5723 (ptp) cc_final: 0.3560 (pp-130) REVERT: A 221 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: A 521 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7397 (mm-40) outliers start: 17 outliers final: 9 residues processed: 116 average time/residue: 1.3546 time to fit residues: 170.9114 Evaluate side-chains 111 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 521 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 143 optimal weight: 0.0770 chunk 86 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 12588 Z= 0.291 Angle : 0.617 9.746 17197 Z= 0.322 Chirality : 0.044 0.208 2004 Planarity : 0.005 0.041 2229 Dihedral : 6.647 85.432 1850 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.15 % Favored : 93.78 % Rotamer: Outliers : 1.74 % Allowed : 15.23 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1609 helix: 0.98 (0.19), residues: 773 sheet: -0.14 (0.42), residues: 159 loop : -1.25 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 8 HIS 0.004 0.001 HIS B 224 PHE 0.016 0.002 PHE C 155 TYR 0.013 0.001 TYR C 176 ARG 0.005 0.000 ARG D 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.335 Fit side-chains revert: symmetry clash REVERT: D 73 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: D 86 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.6941 (ttp-170) REVERT: B 219 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7402 (ttt180) REVERT: C 1 MET cc_start: 0.5889 (ptp) cc_final: 0.3646 (pp-130) REVERT: C 7 PHE cc_start: 0.4533 (OUTLIER) cc_final: 0.4125 (t80) REVERT: A 221 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: A 521 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7437 (mm-40) outliers start: 22 outliers final: 11 residues processed: 108 average time/residue: 1.3493 time to fit residues: 158.5446 Evaluate side-chains 109 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 521 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.166 12588 Z= 0.243 Angle : 0.592 10.004 17197 Z= 0.309 Chirality : 0.043 0.204 2004 Planarity : 0.004 0.043 2229 Dihedral : 6.591 86.483 1850 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.58 % Allowed : 15.71 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.21), residues: 1609 helix: 1.02 (0.19), residues: 777 sheet: -0.14 (0.41), residues: 169 loop : -1.17 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 8 HIS 0.004 0.001 HIS B 224 PHE 0.015 0.001 PHE C 155 TYR 0.010 0.001 TYR C 176 ARG 0.004 0.000 ARG D 316 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: D 73 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: D 86 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.6974 (ttp-170) REVERT: B 219 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7420 (ttt180) REVERT: C 1 MET cc_start: 0.5929 (ptp) cc_final: 0.3700 (pp-130) REVERT: C 7 PHE cc_start: 0.4416 (OUTLIER) cc_final: 0.4042 (t80) REVERT: C 265 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8825 (tp) REVERT: A 221 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: A 521 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7450 (mm-40) outliers start: 20 outliers final: 11 residues processed: 107 average time/residue: 1.3370 time to fit residues: 155.9016 Evaluate side-chains 112 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 521 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN A 161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.086140 restraints weight = 17202.706| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.94 r_work: 0.2813 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 12588 Z= 0.263 Angle : 0.603 10.046 17197 Z= 0.315 Chirality : 0.043 0.213 2004 Planarity : 0.005 0.048 2229 Dihedral : 6.616 85.014 1850 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.42 % Allowed : 15.94 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1609 helix: 1.01 (0.19), residues: 774 sheet: -0.12 (0.42), residues: 169 loop : -1.17 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 8 HIS 0.004 0.001 HIS B 224 PHE 0.015 0.001 PHE C 155 TYR 0.011 0.001 TYR C 176 ARG 0.005 0.000 ARG D 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3863.96 seconds wall clock time: 70 minutes 9.55 seconds (4209.55 seconds total)