Starting phenix.real_space_refine on Sat Nov 18 00:47:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej2_31149/11_2023/7ej2_31149_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej2_31149/11_2023/7ej2_31149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej2_31149/11_2023/7ej2_31149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej2_31149/11_2023/7ej2_31149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej2_31149/11_2023/7ej2_31149_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej2_31149/11_2023/7ej2_31149_updated.pdb" } resolution = 3.3 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 96 5.16 5 C 13488 2.51 5 N 3548 2.21 5 O 3824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 20968 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "B" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2640 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 336} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 179 Chain: "C" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "D" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2640 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 336} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 179 Chain: "E" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "F" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2640 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 336} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 179 Chain: "G" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "H" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2640 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 336} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 179 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.38, per 1000 atoms: 0.50 Number of scatterers: 20968 At special positions: 0 Unit cell: (128.778, 128.778, 157.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 12 15.00 O 3824 8.00 N 3548 7.00 C 13488 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.34 Conformation dependent library (CDL) restraints added in 4.0 seconds 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 16 sheets defined 49.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 66 through 77 removed outlier: 3.658A pdb=" N ALA A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 97 through 106 removed outlier: 4.012A pdb=" N ILE A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 133 through 142 removed outlier: 3.517A pdb=" N ILE A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 192 through 200 removed outlier: 3.754A pdb=" N MET A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 227 No H-bonds generated for 'chain 'A' and resid 224 through 227' Processing helix chain 'A' and resid 229 through 235 removed outlier: 3.786A pdb=" N HIS A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.662A pdb=" N LYS A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 299 removed outlier: 3.546A pdb=" N LYS A 290 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.715A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 4.146A pdb=" N GLU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 333 " --> pdb=" O GLN A 329 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 335 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN A 338 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Proline residue: A 341 - end of helix Processing helix chain 'A' and resid 345 through 355 removed outlier: 3.725A pdb=" N SER A 353 " --> pdb=" O HIS A 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.631A pdb=" N GLN B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 139 Processing helix chain 'B' and resid 154 through 165 removed outlier: 3.592A pdb=" N ASP B 157 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 158 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 160 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR B 161 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER B 165 " --> pdb=" O TYR B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 186 removed outlier: 4.138A pdb=" N GLU B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 200 removed outlier: 3.733A pdb=" N GLU B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 231 through 254 removed outlier: 3.501A pdb=" N ILE B 236 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 238 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 260 No H-bonds generated for 'chain 'B' and resid 257 through 260' Processing helix chain 'B' and resid 299 through 314 removed outlier: 3.610A pdb=" N TRP B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 327 through 330 No H-bonds generated for 'chain 'B' and resid 327 through 330' Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 340 through 343 No H-bonds generated for 'chain 'B' and resid 340 through 343' Processing helix chain 'B' and resid 360 through 378 removed outlier: 3.501A pdb=" N ILE B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE B 375 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 392 removed outlier: 4.068A pdb=" N ILE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 418 removed outlier: 3.749A pdb=" N LEU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 442 removed outlier: 3.590A pdb=" N MET B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 472 removed outlier: 3.502A pdb=" N ILE B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 488 Processing helix chain 'B' and resid 494 through 501 removed outlier: 4.223A pdb=" N TYR B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET B 500 " --> pdb=" O GLN B 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 77 removed outlier: 3.658A pdb=" N ALA C 76 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 97 through 106 removed outlier: 4.011A pdb=" N ILE C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 133 through 142 removed outlier: 3.517A pdb=" N ILE C 137 " --> pdb=" O ARG C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 178 Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.755A pdb=" N MET C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 227 No H-bonds generated for 'chain 'C' and resid 224 through 227' Processing helix chain 'C' and resid 229 through 235 removed outlier: 3.787A pdb=" N HIS C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.662A pdb=" N LYS C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 299 removed outlier: 3.546A pdb=" N LYS C 290 " --> pdb=" O GLN C 286 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 313 removed outlier: 3.715A pdb=" N ALA C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 342 removed outlier: 4.146A pdb=" N GLU C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN C 333 " --> pdb=" O GLN C 329 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE C 337 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN C 338 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 345 through 355 removed outlier: 3.725A pdb=" N SER C 353 " --> pdb=" O HIS C 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.631A pdb=" N GLN D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 139 Processing helix chain 'D' and resid 154 through 165 removed outlier: 3.592A pdb=" N ASP D 157 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA D 158 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU D 160 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR D 161 " --> pdb=" O ALA D 158 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER D 165 " --> pdb=" O TYR D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 186 removed outlier: 4.138A pdb=" N GLU D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 200 removed outlier: 3.733A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP D 200 " --> pdb=" O LYS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 231 through 254 removed outlier: 3.501A pdb=" N ILE D 236 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 238 " --> pdb=" O ARG D 234 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 260 No H-bonds generated for 'chain 'D' and resid 257 through 260' Processing helix chain 'D' and resid 299 through 314 removed outlier: 3.610A pdb=" N TRP D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 327 through 330 No H-bonds generated for 'chain 'D' and resid 327 through 330' Processing helix chain 'D' and resid 333 through 335 No H-bonds generated for 'chain 'D' and resid 333 through 335' Processing helix chain 'D' and resid 340 through 343 No H-bonds generated for 'chain 'D' and resid 340 through 343' Processing helix chain 'D' and resid 360 through 378 removed outlier: 4.159A pdb=" N ARG D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL D 371 " --> pdb=" O ARG D 367 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG D 373 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE D 375 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS D 376 " --> pdb=" O PHE D 372 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU D 377 " --> pdb=" O ARG D 373 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 392 removed outlier: 4.068A pdb=" N ILE D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 418 removed outlier: 3.749A pdb=" N LEU D 400 " --> pdb=" O ARG D 396 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 405 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 442 removed outlier: 3.590A pdb=" N MET D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 removed outlier: 3.502A pdb=" N ILE D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 472 " --> pdb=" O GLY D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 488 Processing helix chain 'D' and resid 494 through 501 removed outlier: 4.223A pdb=" N TYR D 499 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET D 500 " --> pdb=" O GLN D 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 77 removed outlier: 3.659A pdb=" N ALA E 76 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 97 through 106 removed outlier: 4.012A pdb=" N ILE E 102 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 133 through 142 removed outlier: 3.517A pdb=" N ILE E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 178 Processing helix chain 'E' and resid 192 through 200 removed outlier: 3.754A pdb=" N MET E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 227 No H-bonds generated for 'chain 'E' and resid 224 through 227' Processing helix chain 'E' and resid 229 through 235 removed outlier: 3.785A pdb=" N HIS E 234 " --> pdb=" O PRO E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 277 removed outlier: 3.662A pdb=" N LYS E 276 " --> pdb=" O TRP E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 299 removed outlier: 3.546A pdb=" N LYS E 290 " --> pdb=" O GLN E 286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA E 294 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU E 299 " --> pdb=" O ILE E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 313 removed outlier: 3.715A pdb=" N ALA E 309 " --> pdb=" O GLN E 305 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS E 311 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 342 removed outlier: 4.146A pdb=" N GLU E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN E 333 " --> pdb=" O GLN E 329 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY E 335 " --> pdb=" O MET E 331 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA E 336 " --> pdb=" O GLU E 332 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE E 337 " --> pdb=" O ASN E 333 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN E 338 " --> pdb=" O ILE E 334 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL E 339 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Proline residue: E 341 - end of helix Processing helix chain 'E' and resid 345 through 355 removed outlier: 3.725A pdb=" N SER E 353 " --> pdb=" O HIS E 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 removed outlier: 3.630A pdb=" N GLN F 124 " --> pdb=" O LYS F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 139 Processing helix chain 'F' and resid 154 through 165 removed outlier: 3.592A pdb=" N ASP F 157 " --> pdb=" O PRO F 154 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA F 158 " --> pdb=" O SER F 155 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU F 160 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR F 161 " --> pdb=" O ALA F 158 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER F 165 " --> pdb=" O TYR F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 186 removed outlier: 4.138A pdb=" N GLU F 182 " --> pdb=" O ASP F 178 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 184 " --> pdb=" O PHE F 180 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG F 185 " --> pdb=" O SER F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 200 removed outlier: 3.733A pdb=" N GLU F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP F 200 " --> pdb=" O LYS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 221 Processing helix chain 'F' and resid 231 through 254 removed outlier: 3.500A pdb=" N ILE F 236 " --> pdb=" O PRO F 232 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE F 238 " --> pdb=" O ARG F 234 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL F 241 " --> pdb=" O ALA F 237 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU F 242 " --> pdb=" O ILE F 238 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE F 244 " --> pdb=" O SER F 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER F 247 " --> pdb=" O VAL F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 260 No H-bonds generated for 'chain 'F' and resid 257 through 260' Processing helix chain 'F' and resid 299 through 314 removed outlier: 3.610A pdb=" N TRP F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 324 No H-bonds generated for 'chain 'F' and resid 322 through 324' Processing helix chain 'F' and resid 327 through 330 No H-bonds generated for 'chain 'F' and resid 327 through 330' Processing helix chain 'F' and resid 333 through 335 No H-bonds generated for 'chain 'F' and resid 333 through 335' Processing helix chain 'F' and resid 340 through 343 No H-bonds generated for 'chain 'F' and resid 340 through 343' Processing helix chain 'F' and resid 360 through 378 removed outlier: 3.501A pdb=" N ILE F 366 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG F 367 " --> pdb=" O LEU F 363 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL F 371 " --> pdb=" O ARG F 367 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG F 373 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N PHE F 375 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS F 376 " --> pdb=" O PHE F 372 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 392 removed outlier: 4.068A pdb=" N ILE F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 418 removed outlier: 3.749A pdb=" N LEU F 400 " --> pdb=" O ARG F 396 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU F 405 " --> pdb=" O LEU F 401 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE F 406 " --> pdb=" O ILE F 402 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 442 removed outlier: 3.590A pdb=" N MET F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 472 removed outlier: 3.502A pdb=" N ILE F 466 " --> pdb=" O SER F 462 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 470 " --> pdb=" O ILE F 466 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE F 472 " --> pdb=" O GLY F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 Processing helix chain 'F' and resid 494 through 501 removed outlier: 4.223A pdb=" N TYR F 499 " --> pdb=" O GLU F 495 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N MET F 500 " --> pdb=" O GLN F 496 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 77 removed outlier: 3.658A pdb=" N ALA G 76 " --> pdb=" O LEU G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 92 No H-bonds generated for 'chain 'G' and resid 90 through 92' Processing helix chain 'G' and resid 97 through 106 removed outlier: 4.012A pdb=" N ILE G 102 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 133 through 142 removed outlier: 3.517A pdb=" N ILE G 137 " --> pdb=" O ARG G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 178 Processing helix chain 'G' and resid 192 through 200 removed outlier: 3.754A pdb=" N MET G 196 " --> pdb=" O SER G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 227 No H-bonds generated for 'chain 'G' and resid 224 through 227' Processing helix chain 'G' and resid 229 through 235 removed outlier: 3.786A pdb=" N HIS G 234 " --> pdb=" O PRO G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 277 removed outlier: 3.661A pdb=" N LYS G 276 " --> pdb=" O TRP G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 299 removed outlier: 3.546A pdb=" N LYS G 290 " --> pdb=" O GLN G 286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU G 291 " --> pdb=" O ALA G 287 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU G 299 " --> pdb=" O ILE G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 removed outlier: 3.715A pdb=" N ALA G 309 " --> pdb=" O GLN G 305 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS G 311 " --> pdb=" O ALA G 307 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG G 313 " --> pdb=" O ALA G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 342 removed outlier: 4.145A pdb=" N GLU G 332 " --> pdb=" O ASP G 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN G 333 " --> pdb=" O GLN G 329 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY G 335 " --> pdb=" O MET G 331 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA G 336 " --> pdb=" O GLU G 332 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE G 337 " --> pdb=" O ASN G 333 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN G 338 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL G 339 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) Proline residue: G 341 - end of helix Processing helix chain 'G' and resid 345 through 355 removed outlier: 3.725A pdb=" N SER G 353 " --> pdb=" O HIS G 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 124 removed outlier: 3.629A pdb=" N GLN H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 139 Processing helix chain 'H' and resid 154 through 165 removed outlier: 3.592A pdb=" N ASP H 157 " --> pdb=" O PRO H 154 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA H 158 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU H 160 " --> pdb=" O ASP H 157 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR H 161 " --> pdb=" O ALA H 158 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER H 165 " --> pdb=" O TYR H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 186 removed outlier: 4.137A pdb=" N GLU H 182 " --> pdb=" O ASP H 178 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE H 184 " --> pdb=" O PHE H 180 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG H 185 " --> pdb=" O SER H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 200 removed outlier: 3.734A pdb=" N GLU H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP H 200 " --> pdb=" O LYS H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 221 Processing helix chain 'H' and resid 231 through 254 removed outlier: 3.501A pdb=" N ILE H 236 " --> pdb=" O PRO H 232 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA H 237 " --> pdb=" O ALA H 233 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 238 " --> pdb=" O ARG H 234 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL H 241 " --> pdb=" O ALA H 237 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU H 242 " --> pdb=" O ILE H 238 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE H 244 " --> pdb=" O SER H 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER H 247 " --> pdb=" O VAL H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 260 No H-bonds generated for 'chain 'H' and resid 257 through 260' Processing helix chain 'H' and resid 299 through 314 removed outlier: 3.609A pdb=" N TRP H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG H 313 " --> pdb=" O GLU H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 324 No H-bonds generated for 'chain 'H' and resid 322 through 324' Processing helix chain 'H' and resid 327 through 330 No H-bonds generated for 'chain 'H' and resid 327 through 330' Processing helix chain 'H' and resid 333 through 335 No H-bonds generated for 'chain 'H' and resid 333 through 335' Processing helix chain 'H' and resid 340 through 343 No H-bonds generated for 'chain 'H' and resid 340 through 343' Processing helix chain 'H' and resid 360 through 378 removed outlier: 3.500A pdb=" N ILE H 366 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG H 367 " --> pdb=" O LEU H 363 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL H 371 " --> pdb=" O ARG H 367 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE H 372 " --> pdb=" O LEU H 368 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG H 373 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE H 374 " --> pdb=" O ARG H 370 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE H 375 " --> pdb=" O VAL H 371 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS H 376 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU H 377 " --> pdb=" O ARG H 373 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER H 378 " --> pdb=" O ILE H 374 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 392 removed outlier: 4.068A pdb=" N ILE H 386 " --> pdb=" O LYS H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 418 removed outlier: 3.750A pdb=" N LEU H 400 " --> pdb=" O ARG H 396 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU H 405 " --> pdb=" O LEU H 401 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE H 406 " --> pdb=" O ILE H 402 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 442 removed outlier: 3.590A pdb=" N MET H 442 " --> pdb=" O ALA H 438 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 472 removed outlier: 3.502A pdb=" N ILE H 466 " --> pdb=" O SER H 462 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU H 470 " --> pdb=" O ILE H 466 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE H 472 " --> pdb=" O GLY H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 479 through 488 Processing helix chain 'H' and resid 494 through 501 removed outlier: 4.223A pdb=" N TYR H 499 " --> pdb=" O GLU H 495 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET H 500 " --> pdb=" O GLN H 496 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 39 through 41 Processing sheet with id= B, first strand: chain 'A' and resid 52 through 54 removed outlier: 6.217A pdb=" N VAL A 320 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 116 through 119 removed outlier: 6.557A pdb=" N VAL A 154 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE A 119 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE A 156 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR A 184 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ALA A 157 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY A 186 " --> pdb=" O ALA A 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 113 through 118 removed outlier: 6.424A pdb=" N TYR B 147 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 39 through 41 Processing sheet with id= F, first strand: chain 'C' and resid 52 through 54 removed outlier: 6.216A pdb=" N VAL C 320 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 116 through 119 removed outlier: 6.557A pdb=" N VAL C 154 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE C 119 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE C 156 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR C 184 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ALA C 157 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY C 186 " --> pdb=" O ALA C 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 113 through 118 removed outlier: 6.423A pdb=" N TYR D 147 " --> pdb=" O ASN D 109 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 39 through 41 Processing sheet with id= J, first strand: chain 'E' and resid 52 through 54 removed outlier: 6.217A pdb=" N VAL E 320 " --> pdb=" O GLY E 53 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 116 through 119 removed outlier: 6.557A pdb=" N VAL E 154 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE E 119 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE E 156 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR E 184 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ALA E 157 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY E 186 " --> pdb=" O ALA E 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 113 through 118 removed outlier: 6.424A pdb=" N TYR F 147 " --> pdb=" O ASN F 109 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 39 through 41 Processing sheet with id= N, first strand: chain 'G' and resid 52 through 54 removed outlier: 6.217A pdb=" N VAL G 320 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 116 through 119 removed outlier: 6.557A pdb=" N VAL G 154 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE G 119 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE G 156 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR G 184 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ALA G 157 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY G 186 " --> pdb=" O ALA G 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 113 through 118 removed outlier: 6.424A pdb=" N TYR H 147 " --> pdb=" O ASN H 109 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1695 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: 5.83 Time building geometry restraints manager: 8.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3392 1.31 - 1.43: 5730 1.43 - 1.56: 12134 1.56 - 1.68: 20 1.68 - 1.80: 160 Bond restraints: 21436 Sorted by residual: bond pdb=" C1B NAP C 401 " pdb=" C2B NAP C 401 " ideal model delta sigma weight residual 1.528 1.311 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C1B NAP E 401 " pdb=" C2B NAP E 401 " ideal model delta sigma weight residual 1.528 1.311 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C1B NAP G 401 " pdb=" C2B NAP G 401 " ideal model delta sigma weight residual 1.528 1.312 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C1B NAP A 401 " pdb=" C2B NAP A 401 " ideal model delta sigma weight residual 1.528 1.312 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C4D NAP C 401 " pdb=" O4D NAP C 401 " ideal model delta sigma weight residual 1.447 1.307 0.140 2.00e-02 2.50e+03 4.87e+01 ... (remaining 21431 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.47: 469 105.47 - 112.67: 10958 112.67 - 119.87: 7957 119.87 - 127.08: 9497 127.08 - 134.28: 255 Bond angle restraints: 29136 Sorted by residual: angle pdb=" N LEU F 330 " pdb=" CA LEU F 330 " pdb=" C LEU F 330 " ideal model delta sigma weight residual 112.54 120.93 -8.39 1.22e+00 6.72e-01 4.73e+01 angle pdb=" N LEU H 330 " pdb=" CA LEU H 330 " pdb=" C LEU H 330 " ideal model delta sigma weight residual 112.54 120.90 -8.36 1.22e+00 6.72e-01 4.69e+01 angle pdb=" N LEU D 330 " pdb=" CA LEU D 330 " pdb=" C LEU D 330 " ideal model delta sigma weight residual 112.54 120.90 -8.36 1.22e+00 6.72e-01 4.69e+01 angle pdb=" N LEU B 330 " pdb=" CA LEU B 330 " pdb=" C LEU B 330 " ideal model delta sigma weight residual 112.54 120.90 -8.36 1.22e+00 6.72e-01 4.69e+01 angle pdb=" N1A NAP A 401 " pdb=" C6A NAP A 401 " pdb=" N6A NAP A 401 " ideal model delta sigma weight residual 119.30 105.45 13.85 3.00e+00 1.11e-01 2.13e+01 ... (remaining 29131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 11155 16.93 - 33.85: 1173 33.85 - 50.78: 248 50.78 - 67.71: 72 67.71 - 84.63: 36 Dihedral angle restraints: 12684 sinusoidal: 4836 harmonic: 7848 Sorted by residual: dihedral pdb=" N PHE E 120 " pdb=" C PHE E 120 " pdb=" CA PHE E 120 " pdb=" CB PHE E 120 " ideal model delta harmonic sigma weight residual 122.80 132.04 -9.24 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" N PHE A 120 " pdb=" C PHE A 120 " pdb=" CA PHE A 120 " pdb=" CB PHE A 120 " ideal model delta harmonic sigma weight residual 122.80 132.03 -9.23 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" N PHE C 120 " pdb=" C PHE C 120 " pdb=" CA PHE C 120 " pdb=" CB PHE C 120 " ideal model delta harmonic sigma weight residual 122.80 132.03 -9.23 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 12681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3065 0.091 - 0.182: 211 0.182 - 0.273: 12 0.273 - 0.364: 8 0.364 - 0.455: 8 Chirality restraints: 3304 Sorted by residual: chirality pdb=" C2B NAP C 401 " pdb=" C1B NAP C 401 " pdb=" C3B NAP C 401 " pdb=" O2B NAP C 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.30 -0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" C2B NAP E 401 " pdb=" C1B NAP E 401 " pdb=" C3B NAP E 401 " pdb=" O2B NAP E 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.30 -0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" C2B NAP A 401 " pdb=" C1B NAP A 401 " pdb=" C3B NAP A 401 " pdb=" O2B NAP A 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.30 -0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 3301 not shown) Planarity restraints: 3700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 337 " 0.051 5.00e-02 4.00e+02 7.80e-02 9.72e+00 pdb=" N PRO D 338 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 338 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 338 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 337 " 0.051 5.00e-02 4.00e+02 7.78e-02 9.68e+00 pdb=" N PRO B 338 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 338 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 338 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE H 337 " -0.051 5.00e-02 4.00e+02 7.78e-02 9.67e+00 pdb=" N PRO H 338 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO H 338 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO H 338 " -0.042 5.00e-02 4.00e+02 ... (remaining 3697 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6946 2.81 - 3.33: 18448 3.33 - 3.86: 34021 3.86 - 4.38: 40506 4.38 - 4.90: 67767 Nonbonded interactions: 167688 Sorted by model distance: nonbonded pdb=" OH TYR A 184 " pdb=" OE2 GLU G 168 " model vdw 2.290 2.440 nonbonded pdb=" OE2 GLU A 168 " pdb=" OH TYR C 184 " model vdw 2.299 2.440 nonbonded pdb=" OE2 GLU C 168 " pdb=" OH TYR E 184 " model vdw 2.299 2.440 nonbonded pdb=" OG1 THR G 187 " pdb=" OE1 GLU G 213 " model vdw 2.301 2.440 nonbonded pdb=" OG1 THR E 187 " pdb=" OE1 GLU E 213 " model vdw 2.302 2.440 ... (remaining 167683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.010 Extract box with map and model: 10.860 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 55.720 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.140 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: 72.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 : 0.009 0.217 21436 Z= 0.592 Angle : 0.938 13.854 29136 Z= 0.498 Chirality : 0.058 0.455 3304 Planarity : 0.006 0.086 3700 Dihedral : 15.519 84.632 7636 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.78 % Favored : 95.07 % Rotamer: Outliers : 0.19 % Allowed : 18.23 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.99 (0.11), residues: 2696 helix: -4.61 (0.05), residues: 1508 sheet: -2.47 (0.38), residues: 180 loop : -2.81 (0.16), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 551 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 555 average time/residue: 0.4039 time to fit residues: 319.1389 Evaluate side-chains 443 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 443 time to evaluate : 2.460 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 243 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 314 ASN C 204 GLN C 314 ASN E 204 GLN E 314 ASN G 204 GLN G 314 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21436 Z= 0.197 Angle : 0.556 5.821 29136 Z= 0.287 Chirality : 0.041 0.129 3304 Planarity : 0.005 0.051 3700 Dihedral : 6.441 57.762 3024 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.37 % Favored : 97.48 % Rotamer: Outliers : 3.44 % Allowed : 19.85 % Favored : 76.72 % 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: -4.26 (0.13), residues: 2696 helix: -3.23 (0.09), residues: 1476 sheet: -2.06 (0.40), residues: 176 loop : -2.01 (0.18), residues: 1044 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 482 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 37 residues processed: 529 average time/residue: 0.3317 time to fit residues: 267.5666 Evaluate side-chains 472 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 435 time to evaluate : 2.429 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1866 time to fit residues: 16.2770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 67 optimal weight: 0.0870 chunk 243 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 chunk 217 optimal weight: 0.1980 chunk 241 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 314 ASN C 175 HIS E 175 HIS G 175 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21436 Z= 0.186 Angle : 0.540 8.269 29136 Z= 0.267 Chirality : 0.041 0.127 3304 Planarity : 0.004 0.038 3700 Dihedral : 5.993 56.620 3024 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.30 % Favored : 97.55 % Rotamer: Outliers : 1.34 % Allowed : 20.18 % Favored : 78.48 % 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: -3.25 (0.15), residues: 2696 helix: -2.22 (0.12), residues: 1460 sheet: -2.03 (0.39), residues: 176 loop : -1.81 (0.18), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 465 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 491 average time/residue: 0.3374 time to fit residues: 253.0046 Evaluate side-chains 464 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 449 time to evaluate : 2.733 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2085 time to fit residues: 9.1003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 244 optimal weight: 0.0040 chunk 259 optimal weight: 6.9990 chunk 127 optimal weight: 0.4980 chunk 231 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 overall best weight: 2.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 21436 Z= 0.362 Angle : 0.596 8.328 29136 Z= 0.299 Chirality : 0.043 0.149 3304 Planarity : 0.004 0.039 3700 Dihedral : 5.951 59.238 3024 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.82 % Favored : 97.03 % Rotamer: Outliers : 1.67 % Allowed : 21.80 % Favored : 76.53 % 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: -2.79 (0.16), residues: 2696 helix: -1.77 (0.13), residues: 1472 sheet: -2.17 (0.39), residues: 176 loop : -1.65 (0.19), residues: 1048 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 453 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 20 residues processed: 465 average time/residue: 0.3269 time to fit residues: 232.9192 Evaluate side-chains 456 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 436 time to evaluate : 2.446 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2063 time to fit residues: 10.7454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 192 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21436 Z= 0.181 Angle : 0.523 8.709 29136 Z= 0.259 Chirality : 0.040 0.152 3304 Planarity : 0.003 0.036 3700 Dihedral : 5.304 48.362 3024 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.85 % Favored : 98.00 % Rotamer: Outliers : 1.77 % Allowed : 21.52 % Favored : 76.72 % 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: -2.35 (0.16), residues: 2696 helix: -1.45 (0.13), residues: 1488 sheet: -2.13 (0.39), residues: 176 loop : -1.35 (0.19), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 469 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 18 residues processed: 500 average time/residue: 0.3276 time to fit residues: 252.3663 Evaluate side-chains 459 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 441 time to evaluate : 2.201 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1880 time to fit residues: 9.6380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN F 152 ASN H 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 21436 Z= 0.348 Angle : 0.597 8.790 29136 Z= 0.298 Chirality : 0.044 0.203 3304 Planarity : 0.004 0.039 3700 Dihedral : 5.450 47.846 3024 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.74 % Favored : 97.11 % Rotamer: Outliers : 1.62 % Allowed : 22.28 % Favored : 76.10 % 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: -2.29 (0.16), residues: 2696 helix: -1.37 (0.13), residues: 1460 sheet: -2.24 (0.39), residues: 176 loop : -1.36 (0.19), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 445 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 21 residues processed: 461 average time/residue: 0.3440 time to fit residues: 241.8438 Evaluate side-chains 452 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 431 time to evaluate : 2.254 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1875 time to fit residues: 10.6004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 0.0770 chunk 29 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 chunk 146 optimal weight: 0.0870 chunk 218 optimal weight: 0.1980 chunk 144 optimal weight: 0.6980 chunk 258 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 157 optimal weight: 0.4980 chunk 119 optimal weight: 8.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS B 152 ASN C 135 HIS E 135 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21436 Z= 0.146 Angle : 0.540 8.325 29136 Z= 0.266 Chirality : 0.041 0.215 3304 Planarity : 0.003 0.035 3700 Dihedral : 5.057 42.319 3024 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.43 % Allowed : 22.57 % Favored : 77.00 % 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: -2.01 (0.16), residues: 2696 helix: -1.08 (0.14), residues: 1456 sheet: -1.99 (0.47), residues: 136 loop : -1.40 (0.18), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 467 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 474 average time/residue: 0.3471 time to fit residues: 251.8191 Evaluate side-chains 449 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 442 time to evaluate : 2.644 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2411 time to fit residues: 6.7877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 0.0020 chunk 164 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 HIS H 152 ASN ** H 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21436 Z= 0.293 Angle : 0.608 11.140 29136 Z= 0.299 Chirality : 0.043 0.188 3304 Planarity : 0.004 0.038 3700 Dihedral : 5.269 45.272 3024 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.57 % Allowed : 24.57 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.16), residues: 2696 helix: -1.09 (0.14), residues: 1456 sheet: -2.23 (0.39), residues: 176 loop : -1.23 (0.19), residues: 1064 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 443 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 447 average time/residue: 0.3538 time to fit residues: 241.3672 Evaluate side-chains 443 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 435 time to evaluate : 2.423 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1911 time to fit residues: 6.0659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 4.9990 chunk 225 optimal weight: 0.7980 chunk 240 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 0.5980 chunk 227 optimal weight: 0.8980 chunk 239 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21436 Z= 0.179 Angle : 0.567 8.857 29136 Z= 0.279 Chirality : 0.041 0.199 3304 Planarity : 0.003 0.035 3700 Dihedral : 5.043 42.101 3024 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.14 % Allowed : 25.33 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.16), residues: 2696 helix: -0.91 (0.14), residues: 1456 sheet: -1.83 (0.47), residues: 136 loop : -1.28 (0.18), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 455 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 456 average time/residue: 0.3371 time to fit residues: 235.6396 Evaluate side-chains 442 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 440 time to evaluate : 2.309 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2011 time to fit residues: 3.8252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 176 optimal weight: 20.0000 chunk 266 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 212 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 164 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 168 optimal weight: 0.2980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21436 Z= 0.165 Angle : 0.573 10.414 29136 Z= 0.278 Chirality : 0.041 0.220 3304 Planarity : 0.003 0.035 3700 Dihedral : 4.904 41.863 3024 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.33 % Allowed : 25.33 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.16), residues: 2696 helix: -0.74 (0.14), residues: 1460 sheet: -1.65 (0.47), residues: 136 loop : -1.27 (0.18), residues: 1100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 452 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 453 average time/residue: 0.3451 time to fit residues: 238.5023 Evaluate side-chains 443 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 438 time to evaluate : 2.318 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1883 time to fit residues: 4.9242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 89 optimal weight: 0.0970 chunk 218 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 217 GLN ** 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 = 0.3930 r_free = 0.3930 target = 0.154515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107203 restraints weight = 30310.936| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.36 r_work: 0.3053 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21436 Z= 0.185 Angle : 0.587 12.593 29136 Z= 0.281 Chirality : 0.042 0.226 3304 Planarity : 0.003 0.035 3700 Dihedral : 4.881 42.079 3024 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.14 % Allowed : 25.72 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.16), residues: 2696 helix: -0.66 (0.14), residues: 1460 sheet: -1.49 (0.47), residues: 136 loop : -1.25 (0.18), residues: 1100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5414.67 seconds wall clock time: 98 minutes 33.07 seconds (5913.07 seconds total)