Starting phenix.real_space_refine on Mon Feb 19 02:56:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjs_25930/02_2024/7tjs_25930_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjs_25930/02_2024/7tjs_25930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjs_25930/02_2024/7tjs_25930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjs_25930/02_2024/7tjs_25930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjs_25930/02_2024/7tjs_25930_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjs_25930/02_2024/7tjs_25930_updated.pdb" } resolution = 3.2 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= 0.004 sd= 0.242 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 3 5.21 5 S 35 5.16 5 C 14850 2.51 5 N 4092 2.21 5 O 4547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23539 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3631 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 459} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3657 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 3659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3659 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 463} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3512 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 442} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 3515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3515 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3520 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1917 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.35, per 1000 atoms: 0.57 Number of scatterers: 23539 At special positions: 0 Unit cell: (126.828, 126.828, 146.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 12 15.00 Mg 3 11.99 O 4547 8.00 N 4092 7.00 C 14850 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: 9.99 Conformation dependent library (CDL) restraints added in 5.7 seconds 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5636 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 23 sheets defined 44.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.16 Creating SS restraints... Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.911A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 261 Proline residue: A 249 - end of helix removed outlier: 3.690A pdb=" N TRP A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 310 removed outlier: 4.673A pdb=" N PHE A 301 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER A 305 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU A 309 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 310 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 377 through 380 Processing helix chain 'A' and resid 383 through 408 removed outlier: 3.684A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ALA A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N PHE A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.552A pdb=" N ARG A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 454 through 457 removed outlier: 3.972A pdb=" N GLY A 457 " --> pdb=" O HIS A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 454 through 457' Processing helix chain 'A' and resid 460 through 477 removed outlier: 4.893A pdb=" N GLY A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 467 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 471 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS A 475 " --> pdb=" O SER A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.940A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TRP B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 242 through 261 Proline residue: B 249 - end of helix removed outlier: 4.023A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 298 through 310 removed outlier: 3.944A pdb=" N PHE B 301 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER B 305 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG B 306 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU B 309 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.957A pdb=" N LYS B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 392 through 405 removed outlier: 3.687A pdb=" N ALA B 404 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 430 Processing helix chain 'B' and resid 440 through 452 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 460 through 477 removed outlier: 4.660A pdb=" N GLY B 464 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU B 467 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU B 471 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 477 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 488 Processing helix chain 'B' and resid 493 through 508 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.921A pdb=" N GLN C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 224 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 261 Proline residue: C 249 - end of helix removed outlier: 3.520A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 300 through 310 removed outlier: 4.283A pdb=" N ARG C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 377 through 380 Processing helix chain 'C' and resid 383 through 408 removed outlier: 5.450A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LEU C 392 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 393 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU C 394 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 430 Processing helix chain 'C' and resid 440 through 451 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 460 through 477 removed outlier: 4.286A pdb=" N GLY C 464 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU C 467 " --> pdb=" O GLY C 464 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU C 471 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS C 475 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN C 477 " --> pdb=" O LEU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 488 Processing helix chain 'C' and resid 493 through 508 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 163 through 177 removed outlier: 3.795A pdb=" N LYS D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA D 177 " --> pdb=" O ASN D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 203 Processing helix chain 'D' and resid 226 through 247 removed outlier: 4.797A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU D 247 " --> pdb=" O PHE D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 272 Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 285 through 295 removed outlier: 3.959A pdb=" N ARG D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 328 removed outlier: 4.166A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N HIS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 360 through 363 No H-bonds generated for 'chain 'D' and resid 360 through 363' Processing helix chain 'D' and resid 365 through 391 removed outlier: 3.901A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 413 Processing helix chain 'D' and resid 420 through 423 removed outlier: 3.866A pdb=" N VAL D 423 " --> pdb=" O VAL D 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 420 through 423' Processing helix chain 'D' and resid 434 through 445 Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 463 through 473 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 139 through 144 Processing helix chain 'E' and resid 163 through 178 Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 226 through 247 removed outlier: 4.737A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 271 Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 285 through 295 removed outlier: 3.812A pdb=" N LEU E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 320 through 326 Processing helix chain 'E' and resid 337 through 341 Processing helix chain 'E' and resid 360 through 363 No H-bonds generated for 'chain 'E' and resid 360 through 363' Processing helix chain 'E' and resid 365 through 391 removed outlier: 4.961A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 395 No H-bonds generated for 'chain 'E' and resid 393 through 395' Processing helix chain 'E' and resid 398 through 413 Processing helix chain 'E' and resid 421 through 425 Processing helix chain 'E' and resid 434 through 445 Processing helix chain 'E' and resid 454 through 457 Processing helix chain 'E' and resid 463 through 474 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 124 through 126 No H-bonds generated for 'chain 'F' and resid 124 through 126' Processing helix chain 'F' and resid 139 through 144 Processing helix chain 'F' and resid 163 through 177 removed outlier: 4.337A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 204 Processing helix chain 'F' and resid 226 through 245 removed outlier: 3.775A pdb=" N ARG F 231 " --> pdb=" O GLY F 227 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 272 removed outlier: 3.640A pdb=" N GLN F 263 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA F 264 " --> pdb=" O PHE F 261 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ALA F 270 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 280 No H-bonds generated for 'chain 'F' and resid 278 through 280' Processing helix chain 'F' and resid 283 through 293 removed outlier: 4.580A pdb=" N ALA F 286 " --> pdb=" O PRO F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 328 removed outlier: 4.177A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 341 Processing helix chain 'F' and resid 360 through 363 No H-bonds generated for 'chain 'F' and resid 360 through 363' Processing helix chain 'F' and resid 365 through 390 removed outlier: 5.038A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 398 through 414 Processing helix chain 'F' and resid 422 through 425 No H-bonds generated for 'chain 'F' and resid 422 through 425' Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'F' and resid 454 through 457 Processing helix chain 'F' and resid 463 through 473 Processing helix chain 'G' and resid 3 through 55 removed outlier: 4.063A pdb=" N SER G 32 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 101 removed outlier: 3.838A pdb=" N LEU G 91 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 119 Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 185 through 189 Processing helix chain 'G' and resid 205 through 275 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.806A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 98 through 101 Processing sheet with id= C, first strand: chain 'A' and resid 351 through 354 removed outlier: 6.571A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU A 354 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A 170 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 231 through 236 removed outlier: 8.696A pdb=" N ILE A 232 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N HIS A 265 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL A 204 " --> pdb=" O HIS A 265 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU A 267 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL A 206 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL A 269 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL A 208 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP A 271 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SER A 322 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE A 268 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR A 324 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR A 270 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A 326 " --> pdb=" O TYR A 270 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 89 through 91 removed outlier: 6.422A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 98 through 101 Processing sheet with id= G, first strand: chain 'B' and resid 351 through 354 removed outlier: 6.823A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B 354 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 231 through 236 removed outlier: 8.661A pdb=" N ILE B 232 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N HIS B 265 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL B 204 " --> pdb=" O HIS B 265 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU B 267 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL B 206 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 269 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL B 208 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 271 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER B 322 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE B 268 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR B 324 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N TYR B 270 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 326 " --> pdb=" O TYR B 270 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 89 through 91 removed outlier: 6.463A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 98 through 101 Processing sheet with id= K, first strand: chain 'C' and resid 350 through 354 removed outlier: 4.266A pdb=" N ASP C 172 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 231 through 236 removed outlier: 6.578A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER C 322 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE C 268 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR C 324 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N TYR C 270 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.615A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 331 through 334 removed outlier: 7.849A pdb=" N ILE D 153 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER D 306 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU D 155 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN D 308 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLY D 157 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL D 310 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N TYR D 311 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 78 removed outlier: 4.832A pdb=" N ILE E 9 " --> pdb=" O ASP E 78 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 331 through 334 removed outlier: 8.248A pdb=" N ILE E 153 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER E 306 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU E 155 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN E 308 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.547A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 87 removed outlier: 4.842A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 132 through 134 removed outlier: 4.867A pdb=" N GLU F 132 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 331 through 334 removed outlier: 7.554A pdb=" N ILE F 153 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER F 306 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU F 155 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN F 308 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLY F 157 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL F 310 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL F 251 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL F 307 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE F 181 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N PHE F 254 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASP F 256 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR F 185 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 176 through 181 removed outlier: 6.353A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE G 165 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N ILE G 77 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP G 106 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ALA G 76 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL G 108 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR G 109 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER G 129 " --> pdb=" O THR G 109 " (cutoff:3.500A) 962 hydrogen bonds defined for protein. 2649 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: 8.60 Time building geometry restraints manager: 10.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7943 1.34 - 1.46: 2764 1.46 - 1.57: 13109 1.57 - 1.69: 14 1.69 - 1.80: 66 Bond restraints: 23896 Sorted by residual: bond pdb=" O3 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" O4 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.79e+00 bond pdb=" O2 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.567 1.510 0.057 2.00e-02 2.50e+03 8.16e+00 bond pdb=" O1 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.565 1.510 0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" C LYS G 180 " pdb=" N PRO G 181 " ideal model delta sigma weight residual 1.331 1.355 -0.023 1.28e-02 6.10e+03 3.26e+00 ... (remaining 23891 not shown) Histogram of bond angle deviations from ideal: 99.50 - 107.63: 814 107.63 - 115.75: 14985 115.75 - 123.87: 16180 123.87 - 132.00: 409 132.00 - 140.12: 18 Bond angle restraints: 32406 Sorted by residual: angle pdb=" C ASP F 256 " pdb=" N ASN F 257 " pdb=" CA ASN F 257 " ideal model delta sigma weight residual 121.70 128.70 -7.00 1.80e+00 3.09e-01 1.51e+01 angle pdb=" C ASP B 271 " pdb=" N ASP B 272 " pdb=" CA ASP B 272 " ideal model delta sigma weight residual 121.70 127.62 -5.92 1.80e+00 3.09e-01 1.08e+01 angle pdb=" C ASP E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta sigma weight residual 121.70 127.44 -5.74 1.80e+00 3.09e-01 1.02e+01 angle pdb=" C TYR E 281 " pdb=" N GLN E 282 " pdb=" CA GLN E 282 " ideal model delta sigma weight residual 120.39 124.62 -4.23 1.39e+00 5.18e-01 9.26e+00 angle pdb=" CA ARG B 425 " pdb=" CB ARG B 425 " pdb=" CG ARG B 425 " ideal model delta sigma weight residual 114.10 108.06 6.04 2.00e+00 2.50e-01 9.12e+00 ... (remaining 32401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 14295 33.77 - 67.54: 230 67.54 - 101.31: 34 101.31 - 135.09: 0 135.09 - 168.86: 2 Dihedral angle restraints: 14561 sinusoidal: 5754 harmonic: 8807 Sorted by residual: dihedral pdb=" O1B ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PB ADP D 600 " pdb=" PA ADP D 600 " ideal model delta sinusoidal sigma weight residual 300.00 131.14 168.86 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual 300.00 135.30 164.70 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" CA GLU D 294 " pdb=" C GLU D 294 " pdb=" N ARG D 295 " pdb=" CA ARG D 295 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 14558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3286 0.061 - 0.122: 446 0.122 - 0.183: 70 0.183 - 0.243: 2 0.243 - 0.304: 7 Chirality restraints: 3811 Sorted by residual: chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C2' ATP C 600 " pdb=" C1' ATP C 600 " pdb=" C3' ATP C 600 " pdb=" O2' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3808 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 237 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C LEU F 237 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU F 237 " 0.013 2.00e-02 2.50e+03 pdb=" N THR F 238 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS G 180 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO G 181 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO G 181 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 181 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 168 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO G 169 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO G 169 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 169 " -0.020 5.00e-02 4.00e+02 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 47 2.50 - 3.10: 18488 3.10 - 3.70: 34974 3.70 - 4.30: 54991 4.30 - 4.90: 90793 Nonbonded interactions: 199293 Sorted by model distance: nonbonded pdb=" NH1 ARG B 425 " pdb=" O ILE B 458 " model vdw 1.901 2.520 nonbonded pdb=" OG SER A 239 " pdb=" OE2 GLU D 294 " model vdw 1.972 2.440 nonbonded pdb=" O1B ATP C 600 " pdb="MG MG C 601 " model vdw 2.032 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 2.039 2.170 nonbonded pdb=" O3G ATP C 600 " pdb="MG MG C 601 " model vdw 2.058 2.170 ... (remaining 199288 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' and (resid 30 through 315 or (resid 316 and (name N or name CA or nam \ e C or name O or name CB )) or resid 317 through 406 or (resid 407 and (name N o \ r name CA or name C or name O or name CB )) or (resid 410 through 411 and (name \ N or name CA or name C or name O or name CB )) or resid 412 through 416 or (resi \ d 417 and (name N or name CA or name C or name O or name CB )) or resid 418 thro \ ugh 474 or (resid 475 and (name N or name CA or name C or name O or name CB )) o \ r resid 476 through 509 or resid 600 through 601)) selection = (chain 'B' and (resid 30 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 410 or (resid 411 and (name N or n \ ame CA or name C or name O or name CB )) or resid 412 through 466 or (resid 467 \ and (name N or name CA or name C or name O or name CB )) or resid 468 through 47 \ 4 or (resid 475 and (name N or name CA or name C or name O or name CB )) or resi \ d 476 through 479 or (resid 480 and (name N or name CA or name C or name O or na \ me CB )) or resid 481 through 492 or (resid 493 and (name N or name CA or name C \ or name O or name CB )) or resid 494 through 509 or resid 600 through 601)) selection = (chain 'C' and (resid 30 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 315 or (resid 316 and (name N or n \ ame CA or name C or name O or name CB )) or resid 317 through 406 or (resid 407 \ and (name N or name CA or name C or name O or name CB )) or (resid 410 through 4 \ 11 and (name N or name CA or name C or name O or name CB )) or resid 412 through \ 466 or (resid 467 and (name N or name CA or name C or name O or name CB )) or r \ esid 468 through 492 or (resid 493 and (name N or name CA or name C or name O or \ name CB )) or resid 494 through 509 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 9 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 168 or (resid 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 175 or (resid 17 \ 6 through 177 and (name N or name CA or name C or name O or name CB )) or resid \ 178 through 299 or (resid 300 and (name N or name CA or name C or name O or name \ CB )) or resid 301 through 392 or (resid 393 through 396 and (name N or name CA \ or name C or name O or name CB )) or resid 397 or (resid 398 and (name N or nam \ e CA or name C or name O or name CB )) or resid 399 through 474)) selection = (chain 'E' and (resid 9 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 111 or (resid 112 and (name N or na \ me CA or name C or name O or name CB )) or resid 113 through 168 or (resid 169 a \ nd (name N or name CA or name C or name O or name CB )) or resid 170 through 175 \ or (resid 176 through 177 and (name N or name CA or name C or name O or name CB \ )) or resid 178 through 211 or (resid 212 and (name N or name CA or name C or n \ ame O or name CB )) or resid 213 through 381 or (resid 382 and (name N or name C \ A or name C or name O or name CB )) or resid 383 through 474)) selection = (chain 'F' and (resid 9 through 211 or (resid 212 and (name N or name CA or name \ C or name O or name CB )) or resid 213 through 299 or (resid 300 and (name N or \ name CA or name C or name O or name CB )) or resid 301 through 381 or (resid 38 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 383 through \ 392 or (resid 393 through 396 and (name N or name CA or name C or name O or name \ CB )) or resid 397 or (resid 398 and (name N or name CA or name C or name O or \ name CB )) or resid 399 through 474)) } 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: 0.860 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: 5.060 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 66.360 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.003 0.080 23896 Z= 0.182 Angle : 0.605 7.003 32406 Z= 0.327 Chirality : 0.045 0.304 3811 Planarity : 0.004 0.039 4200 Dihedral : 12.985 168.856 8925 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3082 helix: 0.65 (0.14), residues: 1274 sheet: -0.00 (0.23), residues: 504 loop : 0.46 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 258 HIS 0.004 0.001 HIS C 304 PHE 0.012 0.001 PHE B 506 TYR 0.015 0.002 TYR G 212 ARG 0.006 0.001 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7944 (mtp180) REVERT: A 495 LEU cc_start: 0.8839 (tp) cc_final: 0.7970 (tp) REVERT: B 469 SER cc_start: 0.8936 (m) cc_final: 0.8715 (t) REVERT: C 64 MET cc_start: 0.8641 (ttt) cc_final: 0.8394 (ttp) REVERT: C 111 ASP cc_start: 0.8126 (p0) cc_final: 0.7819 (p0) REVERT: C 228 MET cc_start: 0.9067 (tpt) cc_final: 0.8825 (tpt) REVERT: C 462 ARG cc_start: 0.8196 (mtp180) cc_final: 0.7200 (ttt180) REVERT: D 277 SER cc_start: 0.8263 (t) cc_final: 0.8052 (t) REVERT: D 339 ILE cc_start: 0.9063 (mm) cc_final: 0.8841 (mt) REVERT: D 342 LEU cc_start: 0.9078 (mt) cc_final: 0.8867 (mp) REVERT: D 381 TYR cc_start: 0.9046 (t80) cc_final: 0.8649 (t80) REVERT: D 393 MET cc_start: 0.6195 (mtp) cc_final: 0.5742 (mtp) REVERT: E 64 MET cc_start: 0.8702 (mmt) cc_final: 0.8491 (mmt) REVERT: E 222 MET cc_start: 0.8506 (mtt) cc_final: 0.8175 (mtt) REVERT: E 381 TYR cc_start: 0.8525 (t80) cc_final: 0.8106 (t80) REVERT: F 386 ASP cc_start: 0.7377 (m-30) cc_final: 0.7140 (m-30) REVERT: F 391 LEU cc_start: 0.8711 (mt) cc_final: 0.8509 (mt) REVERT: F 459 MET cc_start: 0.8949 (mmt) cc_final: 0.8633 (mmt) REVERT: G 15 ASN cc_start: 0.8323 (t0) cc_final: 0.8054 (t0) REVERT: G 145 LEU cc_start: 0.7710 (mp) cc_final: 0.6977 (tp) REVERT: G 211 GLU cc_start: 0.6364 (mt-10) cc_final: 0.5576 (tt0) REVERT: G 229 GLU cc_start: 0.8339 (tt0) cc_final: 0.8123 (tt0) outliers start: 0 outliers final: 0 residues processed: 475 average time/residue: 0.4232 time to fit residues: 296.0681 Evaluate side-chains 240 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 259 optimal weight: 4.9990 chunk 232 optimal weight: 0.0570 chunk 129 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 278 optimal weight: 3.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS B 26 ASN B 67 ASN C 220 GLN C 304 HIS D 172 ASN D 385 GLN E 263 GLN E 385 GLN E 455 HIS F 178 HIS G 49 GLN G 216 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23896 Z= 0.191 Angle : 0.552 8.630 32406 Z= 0.282 Chirality : 0.045 0.261 3811 Planarity : 0.004 0.041 4200 Dihedral : 7.347 157.095 3445 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.17 % Allowed : 5.90 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.12 (0.15), residues: 3082 helix: 1.35 (0.15), residues: 1268 sheet: 0.16 (0.23), residues: 494 loop : 0.56 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 191 HIS 0.004 0.001 HIS D 367 PHE 0.023 0.001 PHE C 466 TYR 0.024 0.001 TYR A 473 ARG 0.007 0.000 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 269 time to evaluate : 2.885 Fit side-chains REVERT: B 469 SER cc_start: 0.8868 (m) cc_final: 0.8667 (t) REVERT: C 228 MET cc_start: 0.9025 (tpt) cc_final: 0.8809 (tpt) REVERT: C 462 ARG cc_start: 0.8203 (mtp180) cc_final: 0.7189 (ttt180) REVERT: D 393 MET cc_start: 0.6024 (mtp) cc_final: 0.5709 (mtp) REVERT: D 412 ARG cc_start: 0.8332 (mtt90) cc_final: 0.8025 (mtt90) REVERT: E 64 MET cc_start: 0.8703 (mmt) cc_final: 0.8386 (mmt) REVERT: F 208 ASN cc_start: 0.6982 (t0) cc_final: 0.6727 (t0) REVERT: F 459 MET cc_start: 0.8866 (mmt) cc_final: 0.8620 (mmm) REVERT: G 15 ASN cc_start: 0.8195 (t0) cc_final: 0.7751 (t0) REVERT: G 120 ARG cc_start: 0.8364 (ptt90) cc_final: 0.8048 (ptt90) outliers start: 29 outliers final: 21 residues processed: 289 average time/residue: 0.3724 time to fit residues: 167.0150 Evaluate side-chains 241 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 220 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain F residue 197 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 154 optimal weight: 0.5980 chunk 86 optimal weight: 0.0020 chunk 232 optimal weight: 0.1980 chunk 189 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 279 optimal weight: 0.9990 chunk 301 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 276 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 304 HIS D 328 HIS E 455 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 23896 Z= 0.145 Angle : 0.492 8.718 32406 Z= 0.250 Chirality : 0.043 0.260 3811 Planarity : 0.004 0.041 4200 Dihedral : 6.752 171.100 3445 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.17 % Allowed : 7.27 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.44 (0.16), residues: 3082 helix: 1.71 (0.15), residues: 1262 sheet: 0.38 (0.23), residues: 493 loop : 0.62 (0.18), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 191 HIS 0.003 0.001 HIS D 367 PHE 0.017 0.001 PHE C 466 TYR 0.015 0.001 TYR D 458 ARG 0.006 0.000 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 258 time to evaluate : 2.761 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8652 (mtt-85) cc_final: 0.8379 (mtt90) REVERT: B 26 ASN cc_start: 0.6276 (OUTLIER) cc_final: 0.6012 (p0) REVERT: B 82 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8126 (ttt90) REVERT: B 89 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8212 (tp) REVERT: C 228 MET cc_start: 0.9017 (tpt) cc_final: 0.8779 (tpt) REVERT: C 271 ASP cc_start: 0.8595 (t0) cc_final: 0.8336 (t0) REVERT: C 462 ARG cc_start: 0.8185 (mtp180) cc_final: 0.7250 (ttt180) REVERT: E 64 MET cc_start: 0.8720 (mmt) cc_final: 0.8355 (mmt) REVERT: F 385 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7403 (tp-100) REVERT: F 459 MET cc_start: 0.8806 (mmt) cc_final: 0.8569 (mmm) REVERT: G 15 ASN cc_start: 0.8115 (t0) cc_final: 0.7683 (t0) REVERT: G 120 ARG cc_start: 0.8320 (ptt90) cc_final: 0.8094 (ptt90) REVERT: G 145 LEU cc_start: 0.7560 (mt) cc_final: 0.6828 (tp) outliers start: 29 outliers final: 14 residues processed: 277 average time/residue: 0.3614 time to fit residues: 156.1530 Evaluate side-chains 230 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 212 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain F residue 385 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 275 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 280 optimal weight: 0.7980 chunk 296 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 265 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 379 GLN F 379 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23896 Z= 0.217 Angle : 0.508 8.111 32406 Z= 0.258 Chirality : 0.044 0.283 3811 Planarity : 0.004 0.042 4200 Dihedral : 6.657 177.885 3445 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.49 % Allowed : 8.32 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.40 (0.16), residues: 3082 helix: 1.74 (0.15), residues: 1258 sheet: 0.19 (0.23), residues: 514 loop : 0.59 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 191 HIS 0.008 0.001 HIS A 478 PHE 0.014 0.001 PHE C 466 TYR 0.016 0.001 TYR D 458 ARG 0.009 0.000 ARG D 412 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 229 time to evaluate : 2.841 Fit side-chains revert: symmetry clash REVERT: B 26 ASN cc_start: 0.6443 (OUTLIER) cc_final: 0.6059 (p0) REVERT: B 82 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8137 (ttt90) REVERT: B 89 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8202 (tp) REVERT: C 228 MET cc_start: 0.9027 (tpt) cc_final: 0.8806 (tpt) REVERT: C 271 ASP cc_start: 0.8618 (t0) cc_final: 0.8360 (t0) REVERT: C 462 ARG cc_start: 0.8253 (mtp180) cc_final: 0.7270 (ttt180) REVERT: E 64 MET cc_start: 0.8731 (mmt) cc_final: 0.8360 (mmt) REVERT: F 237 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8160 (mp) REVERT: F 459 MET cc_start: 0.8856 (mmt) cc_final: 0.8632 (mmm) REVERT: G 15 ASN cc_start: 0.8129 (t0) cc_final: 0.7685 (t0) REVERT: G 120 ARG cc_start: 0.8331 (ptt90) cc_final: 0.8019 (ptt90) REVERT: G 145 LEU cc_start: 0.7645 (mt) cc_final: 0.6781 (tp) outliers start: 37 outliers final: 22 residues processed: 257 average time/residue: 0.3731 time to fit residues: 149.8848 Evaluate side-chains 238 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 212 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 237 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 247 optimal weight: 0.3980 chunk 168 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 220 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 151 optimal weight: 0.6980 chunk 266 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS B 452 ASN E 455 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23896 Z= 0.163 Angle : 0.480 10.426 32406 Z= 0.243 Chirality : 0.042 0.207 3811 Planarity : 0.003 0.042 4200 Dihedral : 6.404 173.073 3445 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.17 % Allowed : 8.89 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.44 (0.16), residues: 3082 helix: 1.80 (0.15), residues: 1266 sheet: 0.19 (0.23), residues: 526 loop : 0.60 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 191 HIS 0.006 0.001 HIS A 478 PHE 0.012 0.001 PHE C 466 TYR 0.015 0.001 TYR G 159 ARG 0.008 0.000 ARG D 412 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 234 time to evaluate : 3.051 Fit side-chains revert: symmetry clash REVERT: B 26 ASN cc_start: 0.6433 (OUTLIER) cc_final: 0.5956 (p0) REVERT: B 82 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8112 (ttt90) REVERT: B 89 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8216 (tp) REVERT: B 385 LEU cc_start: 0.8770 (mt) cc_final: 0.8538 (mm) REVERT: C 228 MET cc_start: 0.9036 (tpt) cc_final: 0.8823 (tpt) REVERT: C 271 ASP cc_start: 0.8559 (t0) cc_final: 0.8307 (t0) REVERT: C 462 ARG cc_start: 0.8237 (mtp180) cc_final: 0.7318 (ttt-90) REVERT: E 64 MET cc_start: 0.8744 (mmt) cc_final: 0.8395 (mmt) REVERT: E 356 ARG cc_start: 0.8148 (mmm-85) cc_final: 0.7733 (mtp85) REVERT: F 237 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8101 (mp) REVERT: G 15 ASN cc_start: 0.8090 (t0) cc_final: 0.7644 (t0) REVERT: G 145 LEU cc_start: 0.7361 (mt) cc_final: 0.6599 (tp) outliers start: 29 outliers final: 18 residues processed: 255 average time/residue: 0.3370 time to fit residues: 137.8359 Evaluate side-chains 221 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 199 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 223 ASN Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 237 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 99 optimal weight: 4.9990 chunk 267 optimal weight: 0.0270 chunk 58 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 HIS F 385 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23896 Z= 0.274 Angle : 0.520 8.899 32406 Z= 0.263 Chirality : 0.044 0.323 3811 Planarity : 0.004 0.043 4200 Dihedral : 6.442 166.521 3445 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.54 % Allowed : 9.41 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.28 (0.16), residues: 3082 helix: 1.69 (0.15), residues: 1264 sheet: 0.06 (0.23), residues: 516 loop : 0.50 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 191 HIS 0.005 0.001 HIS E 367 PHE 0.011 0.001 PHE A 506 TYR 0.014 0.001 TYR D 458 ARG 0.009 0.000 ARG D 412 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 217 time to evaluate : 2.784 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.8273 (ptm) cc_final: 0.7936 (ttp) REVERT: B 26 ASN cc_start: 0.6566 (OUTLIER) cc_final: 0.6173 (p0) REVERT: B 82 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.7995 (ttt90) REVERT: B 89 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8246 (tp) REVERT: C 462 ARG cc_start: 0.8288 (mtp180) cc_final: 0.7279 (ttt-90) REVERT: C 493 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8390 (ttmm) REVERT: E 64 MET cc_start: 0.8764 (mmt) cc_final: 0.8390 (mmt) REVERT: E 356 ARG cc_start: 0.8142 (mmm-85) cc_final: 0.7841 (mtp85) REVERT: G 15 ASN cc_start: 0.8165 (t0) cc_final: 0.7677 (t0) REVERT: G 120 ARG cc_start: 0.8189 (ptt90) cc_final: 0.7943 (ptt90) REVERT: G 145 LEU cc_start: 0.7336 (mt) cc_final: 0.6668 (tp) outliers start: 38 outliers final: 26 residues processed: 246 average time/residue: 0.3602 time to fit residues: 139.2245 Evaluate side-chains 230 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 201 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 11 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 286 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 295 optimal weight: 20.0000 chunk 185 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 221 GLN F 385 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23896 Z= 0.251 Angle : 0.510 8.265 32406 Z= 0.258 Chirality : 0.044 0.266 3811 Planarity : 0.004 0.045 4200 Dihedral : 6.361 159.907 3445 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.58 % Allowed : 9.66 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.23 (0.16), residues: 3082 helix: 1.67 (0.15), residues: 1266 sheet: 0.04 (0.23), residues: 526 loop : 0.45 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 191 HIS 0.006 0.001 HIS A 304 PHE 0.028 0.001 PHE C 466 TYR 0.013 0.001 TYR D 381 ARG 0.008 0.000 ARG D 412 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 211 time to evaluate : 3.034 Fit side-chains REVERT: A 320 SER cc_start: 0.8773 (m) cc_final: 0.8532 (t) REVERT: B 26 ASN cc_start: 0.6619 (OUTLIER) cc_final: 0.6153 (p0) REVERT: B 82 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.7909 (ttt90) REVERT: B 89 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8257 (tp) REVERT: C 462 ARG cc_start: 0.8250 (mtp180) cc_final: 0.7256 (ttt-90) REVERT: E 64 MET cc_start: 0.8729 (mmt) cc_final: 0.8367 (mmt) REVERT: E 356 ARG cc_start: 0.8167 (mmm-85) cc_final: 0.7692 (mtp85) REVERT: G 15 ASN cc_start: 0.8163 (t0) cc_final: 0.7675 (t0) REVERT: G 120 ARG cc_start: 0.8178 (ptt90) cc_final: 0.7929 (ptt90) REVERT: G 145 LEU cc_start: 0.7346 (mt) cc_final: 0.6684 (tp) outliers start: 39 outliers final: 29 residues processed: 243 average time/residue: 0.3724 time to fit residues: 140.2941 Evaluate side-chains 233 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 197 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 183 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 201 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 HIS E 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23896 Z= 0.323 Angle : 0.549 7.936 32406 Z= 0.278 Chirality : 0.045 0.256 3811 Planarity : 0.004 0.045 4200 Dihedral : 6.466 156.431 3445 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.70 % Allowed : 9.78 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.04 (0.16), residues: 3082 helix: 1.55 (0.15), residues: 1264 sheet: -0.15 (0.23), residues: 529 loop : 0.36 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 191 HIS 0.005 0.001 HIS E 367 PHE 0.021 0.001 PHE C 466 TYR 0.015 0.002 TYR D 381 ARG 0.008 0.000 ARG D 412 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 208 time to evaluate : 2.942 Fit side-chains REVERT: B 26 ASN cc_start: 0.6804 (OUTLIER) cc_final: 0.6331 (p0) REVERT: B 82 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.7855 (ttt90) REVERT: B 89 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8290 (tp) REVERT: B 494 GLU cc_start: 0.6735 (tm-30) cc_final: 0.6425 (tm-30) REVERT: C 462 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7268 (ttt180) REVERT: E 64 MET cc_start: 0.8733 (mmt) cc_final: 0.8359 (mmt) REVERT: G 15 ASN cc_start: 0.8177 (t0) cc_final: 0.7715 (t0) REVERT: G 145 LEU cc_start: 0.7317 (mt) cc_final: 0.6643 (tp) outliers start: 42 outliers final: 31 residues processed: 242 average time/residue: 0.3955 time to fit residues: 149.8167 Evaluate side-chains 240 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 206 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 197 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 269 optimal weight: 4.9990 chunk 283 optimal weight: 5.9990 chunk 258 optimal weight: 1.9990 chunk 275 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 216 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 249 optimal weight: 0.8980 chunk 260 optimal weight: 0.9980 chunk 274 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 ASN E 249 GLN F 385 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23896 Z= 0.228 Angle : 0.515 8.216 32406 Z= 0.261 Chirality : 0.044 0.231 3811 Planarity : 0.004 0.046 4200 Dihedral : 6.306 153.143 3445 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.41 % Allowed : 10.10 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.12 (0.16), residues: 3082 helix: 1.61 (0.15), residues: 1278 sheet: -0.10 (0.23), residues: 510 loop : 0.38 (0.18), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 191 HIS 0.006 0.001 HIS E 455 PHE 0.023 0.001 PHE C 466 TYR 0.012 0.001 TYR D 458 ARG 0.007 0.000 ARG D 412 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 212 time to evaluate : 2.902 Fit side-chains revert: symmetry clash REVERT: A 320 SER cc_start: 0.8793 (m) cc_final: 0.8563 (t) REVERT: B 26 ASN cc_start: 0.6778 (OUTLIER) cc_final: 0.6259 (p0) REVERT: B 82 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.7823 (ttt90) REVERT: B 89 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8276 (tp) REVERT: B 420 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7200 (mp) REVERT: B 494 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6520 (tm-30) REVERT: C 462 ARG cc_start: 0.8157 (mtp180) cc_final: 0.7260 (ttt-90) REVERT: E 64 MET cc_start: 0.8712 (mmt) cc_final: 0.8346 (mmt) REVERT: G 15 ASN cc_start: 0.8134 (t0) cc_final: 0.7669 (t0) REVERT: G 145 LEU cc_start: 0.7359 (mt) cc_final: 0.6654 (tp) outliers start: 35 outliers final: 28 residues processed: 241 average time/residue: 0.3676 time to fit residues: 139.0333 Evaluate side-chains 228 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain F residue 133 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 181 optimal weight: 0.9990 chunk 291 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 281 optimal weight: 0.8980 chunk 243 optimal weight: 0.0010 chunk 25 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 455 HIS F 385 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23896 Z= 0.179 Angle : 0.493 7.940 32406 Z= 0.249 Chirality : 0.043 0.227 3811 Planarity : 0.003 0.045 4200 Dihedral : 6.076 149.437 3445 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.29 % Allowed : 10.30 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.23 (0.16), residues: 3082 helix: 1.69 (0.15), residues: 1284 sheet: -0.08 (0.24), residues: 495 loop : 0.45 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 191 HIS 0.003 0.001 HIS E 367 PHE 0.023 0.001 PHE C 466 TYR 0.011 0.001 TYR D 458 ARG 0.008 0.000 ARG A 400 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 2.893 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.8250 (ptm) cc_final: 0.7930 (ttp) REVERT: A 320 SER cc_start: 0.8755 (m) cc_final: 0.8549 (t) REVERT: B 26 ASN cc_start: 0.6770 (OUTLIER) cc_final: 0.6263 (p0) REVERT: B 82 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.7921 (ttt90) REVERT: B 89 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8259 (tp) REVERT: B 420 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7149 (mp) REVERT: B 494 GLU cc_start: 0.6831 (tm-30) cc_final: 0.6543 (tm-30) REVERT: C 393 LYS cc_start: 0.7673 (tptt) cc_final: 0.7412 (tttt) REVERT: C 462 ARG cc_start: 0.8142 (mtp180) cc_final: 0.7244 (ttt-90) REVERT: E 64 MET cc_start: 0.8693 (mmt) cc_final: 0.8325 (mmt) REVERT: G 15 ASN cc_start: 0.8123 (t0) cc_final: 0.7633 (t0) REVERT: G 145 LEU cc_start: 0.7478 (mt) cc_final: 0.6776 (tp) outliers start: 32 outliers final: 25 residues processed: 232 average time/residue: 0.3511 time to fit residues: 129.3525 Evaluate side-chains 222 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 422 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 193 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.093719 restraints weight = 30484.887| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.80 r_work: 0.2942 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23896 Z= 0.350 Angle : 0.561 7.369 32406 Z= 0.284 Chirality : 0.046 0.231 3811 Planarity : 0.004 0.046 4200 Dihedral : 6.319 150.670 3445 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.25 % Allowed : 10.67 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.16), residues: 3082 helix: 1.54 (0.15), residues: 1265 sheet: -0.26 (0.23), residues: 517 loop : 0.30 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 191 HIS 0.006 0.001 HIS E 367 PHE 0.025 0.002 PHE C 466 TYR 0.013 0.001 TYR D 449 ARG 0.009 0.000 ARG A 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4859.22 seconds wall clock time: 89 minutes 12.55 seconds (5352.55 seconds total)