Starting phenix.real_space_refine on Sun Feb 18 23:47:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjv_25933/02_2024/7tjv_25933_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjv_25933/02_2024/7tjv_25933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjv_25933/02_2024/7tjv_25933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjv_25933/02_2024/7tjv_25933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjv_25933/02_2024/7tjv_25933_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjv_25933/02_2024/7tjv_25933_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 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 14 5.49 5 Mg 5 5.21 5 S 35 5.16 5 C 14649 2.51 5 N 4084 2.21 5 O 4383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23170 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3585 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 459} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 3584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3584 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 456} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 3577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3577 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 463} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 14, 'HIS:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 85 Chain: "D" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3468 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 443} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "E" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3389 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 16, 'ARG:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 106 Chain: "F" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3488 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "G" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1923 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 81 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.25, per 1000 atoms: 0.53 Number of scatterers: 23170 At special positions: 0 Unit cell: (125.317, 128.012, 156.31, 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 14 15.00 Mg 5 11.99 O 4383 8.00 N 4084 7.00 C 14649 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: 9.13 Conformation dependent library (CDL) restraints added in 4.6 seconds 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5650 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 23 sheets defined 43.9% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.03 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 153 through 158 Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.929A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.521A pdb=" N ALA A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 242 through 261 Proline residue: A 249 - end of helix removed outlier: 3.844A 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: 3.823A pdb=" N PHE A 301 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 305 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 306 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU A 309 " --> pdb=" O ARG A 306 " (cutoff:3.500A) 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 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 383 through 411 removed outlier: 4.086A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N PHE A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N PHE A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY A 409 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ASP A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 429 removed outlier: 3.560A pdb=" N ARG A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 454 through 457 removed outlier: 3.981A 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: 4.219A pdb=" N GLY A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 467 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 471 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 476 " --> pdb=" O TYR A 473 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 477 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 removed outlier: 3.660A pdb=" N GLU A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 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 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 177 through 192 removed outlier: 4.046A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 5.328A 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: 3.609A pdb=" N TRP B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.252A 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: 4.245A pdb=" N PHE B 301 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU B 309 " --> pdb=" O ARG B 306 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 310 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 356 through 359 No H-bonds generated for 'chain 'B' and resid 356 through 359' Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 392 through 403 removed outlier: 3.611A pdb=" N ALA B 397 " --> pdb=" O LYS B 393 " (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 454 through 457 Processing helix chain 'B' and resid 460 through 476 removed outlier: 4.870A pdb=" N GLY B 464 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU B 471 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 493 through 507 Processing helix chain 'C' and resid 81 through 83 No H-bonds generated for 'chain 'C' and resid 81 through 83' 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: 4.273A pdb=" N GLN C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 5.320A 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 242 through 261 Proline residue: C 249 - end of helix removed outlier: 3.706A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.442A 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 298 through 310 removed outlier: 3.989A pdb=" N PHE C 301 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 303 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG C 306 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU C 309 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.575A pdb=" N TYR C 360 " --> pdb=" O ALA C 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 356 through 360' Processing helix chain 'C' and resid 377 through 380 Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 392 through 408 removed outlier: 3.602A pdb=" N GLU C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 3.925A 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 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 460 through 477 removed outlier: 3.529A pdb=" N ILE C 463 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY C 464 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 467 " --> pdb=" O GLY C 464 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 468 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE C 470 " --> pdb=" O GLU C 467 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU C 471 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS C 475 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN C 477 " --> pdb=" O LEU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 487 Processing helix chain 'C' and resid 493 through 507 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 139 through 144 Processing helix chain 'D' and resid 163 through 173 Processing helix chain 'D' and resid 191 through 203 Processing helix chain 'D' and resid 226 through 245 removed outlier: 4.937A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 271 removed outlier: 3.668A pdb=" N ALA D 264 " --> pdb=" O PHE D 261 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL D 268 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA D 270 " --> pdb=" O GLU D 267 " (cutoff:3.500A) 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 283 through 295 removed outlier: 4.612A pdb=" N ALA D 286 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 288 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU D 294 " --> 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: 4.388A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 4.795A 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: 4.575A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 395 No H-bonds generated for 'chain 'D' and resid 393 through 395' Processing helix chain 'D' and resid 398 through 413 Processing helix chain 'D' and resid 420 through 425 removed outlier: 4.029A pdb=" N VAL D 423 " --> pdb=" O VAL D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 446 removed outlier: 3.519A pdb=" N ALA D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 456 No H-bonds generated for 'chain 'D' and resid 454 through 456' Processing helix chain 'D' and resid 463 through 474 removed outlier: 4.003A pdb=" N ALA D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) 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 177 removed outlier: 3.811A pdb=" N ALA E 175 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS E 176 " --> pdb=" O ASN E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 226 through 247 removed outlier: 5.141A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA E 240 " --> pdb=" O GLY E 236 " (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 293 removed outlier: 3.797A pdb=" N LEU E 292 " --> pdb=" O ASP E 288 " (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: 4.014A pdb=" N VAL E 370 " --> pdb=" O GLU E 366 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE E 390 " --> pdb=" O ASP E 386 " (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 414 removed outlier: 4.180A pdb=" N ARG E 406 " --> pdb=" O LEU E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 425 No H-bonds generated for 'chain 'E' and resid 422 through 425' Processing helix chain 'E' and resid 434 through 445 removed outlier: 3.605A pdb=" N PHE E 441 " --> pdb=" O THR E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 457 No H-bonds generated for '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: 5.043A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 226 through 245 removed outlier: 4.896A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 272 removed outlier: 3.608A pdb=" N ALA F 264 " --> pdb=" O PHE F 261 " (cutoff:3.500A) removed outlier: 4.377A 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 296 removed outlier: 4.506A pdb=" N ALA F 286 " --> pdb=" O PRO F 283 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP F 288 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET F 289 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU F 294 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG F 295 " --> pdb=" O LEU F 292 " (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: 4.424A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.834A 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 391 removed outlier: 3.702A pdb=" N GLN F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.441A 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 413 Processing helix chain 'F' and resid 419 through 425 removed outlier: 4.455A pdb=" N VAL F 423 " --> pdb=" O VAL F 420 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR F 425 " --> pdb=" O GLU F 422 " (cutoff:3.500A) 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: 3.791A pdb=" N ARG G 9 " --> pdb=" O GLU G 5 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TYR G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 101 removed outlier: 3.999A pdb=" N HIS G 88 " --> pdb=" O GLY G 85 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN G 90 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU G 91 " --> pdb=" O HIS G 88 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS G 93 " --> pdb=" O GLN G 90 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG G 96 " --> pdb=" O LYS G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 120 removed outlier: 4.479A pdb=" N ARG G 120 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 135 No H-bonds generated for 'chain 'G' and resid 133 through 135' Processing helix chain 'G' and resid 140 through 153 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 190 removed outlier: 3.586A pdb=" N GLU G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 274 removed outlier: 4.013A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP G 269 " --> pdb=" O ASN G 265 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE G 270 " --> pdb=" O GLU G 266 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.936A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.610A 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 109 through 111 removed outlier: 8.605A pdb=" N VAL A 110 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE A 233 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER A 322 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE A 268 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR A 324 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N TYR A 270 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 350 through 354 removed outlier: 4.247A pdb=" N ASP A 172 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 30 through 32 removed outlier: 6.404A pdb=" N GLY B 74 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU B 68 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N PHE B 44 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VAL B 33 " --> pdb=" O PHE B 44 " (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 109 through 111 removed outlier: 8.677A pdb=" N VAL B 110 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE B 233 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER B 322 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE B 268 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR B 324 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N TYR B 270 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 326 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 350 through 354 Processing sheet with id= I, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.417A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU C 68 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLN C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N PHE C 44 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N VAL C 33 " --> pdb=" O PHE C 44 " (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 108 through 110 removed outlier: 4.102A pdb=" N ARG C 108 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 167 through 171 removed outlier: 6.557A pdb=" N GLY C 350 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE C 170 " --> pdb=" O GLY C 350 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE C 352 " --> pdb=" O ILE C 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 12 through 17 removed outlier: 6.669A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.683A 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 87 removed outlier: 4.908A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 331 through 334 removed outlier: 3.644A pdb=" N ALA D 331 " --> pdb=" O LYS D 152 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ILE D 153 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER D 306 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU D 155 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN D 308 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N GLY D 157 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL D 310 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N TYR D 311 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE D 181 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N PHE D 254 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL D 183 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP D 256 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR D 185 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA D 216 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLY D 186 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL D 218 " --> pdb=" O GLY D 186 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLY D 188 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLY D 220 " --> pdb=" O GLY D 188 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.413A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.490A 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 306 through 309 removed outlier: 6.647A pdb=" N ALA E 331 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N PHE E 156 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR E 333 " --> pdb=" O PHE E 156 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 252 through 256 Processing sheet with id= T, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.701A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 84 through 87 removed outlier: 3.649A pdb=" N VAL F 87 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 152 through 157 removed outlier: 7.803A pdb=" N ILE F 153 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER F 306 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU F 155 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLN F 308 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY F 157 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL F 310 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL F 251 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL F 307 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE F 181 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N PHE F 254 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ASP F 256 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR F 185 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 106 through 110 removed outlier: 5.373A pdb=" N ASN G 167 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE G 164 " --> pdb=" O LYS G 180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS G 180 " --> pdb=" O ILE G 164 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) 937 hydrogen bonds defined for protein. 2490 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: 8.53 Time building geometry restraints manager: 9.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4617 1.33 - 1.45: 5008 1.45 - 1.57: 13812 1.57 - 1.69: 24 1.69 - 1.81: 66 Bond restraints: 23527 Sorted by residual: bond pdb=" N PRO C 297 " pdb=" CD PRO C 297 " ideal model delta sigma weight residual 1.473 1.435 0.038 1.40e-02 5.10e+03 7.28e+00 bond pdb=" CZ ARG C 306 " pdb=" NH2 ARG C 306 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.23e+00 bond pdb=" C LEU A 308 " pdb=" O LEU A 308 " ideal model delta sigma weight residual 1.237 1.208 0.028 1.19e-02 7.06e+03 5.71e+00 bond pdb=" CZ ARG A 306 " pdb=" NH2 ARG A 306 " ideal model delta sigma weight residual 1.330 1.300 0.030 1.30e-02 5.92e+03 5.42e+00 bond pdb=" N PRO A 297 " pdb=" CD PRO A 297 " ideal model delta sigma weight residual 1.473 1.443 0.030 1.40e-02 5.10e+03 4.63e+00 ... (remaining 23522 not shown) Histogram of bond angle deviations from ideal: 99.53 - 107.58: 823 107.58 - 115.62: 14721 115.62 - 123.67: 15912 123.67 - 131.72: 482 131.72 - 139.76: 21 Bond angle restraints: 31959 Sorted by residual: angle pdb=" CA ASP A 299 " pdb=" C ASP A 299 " pdb=" N VAL A 300 " ideal model delta sigma weight residual 116.84 123.47 -6.63 1.71e+00 3.42e-01 1.51e+01 angle pdb=" CB HIS C 304 " pdb=" CG HIS C 304 " pdb=" CD2 HIS C 304 " ideal model delta sigma weight residual 131.20 126.28 4.92 1.30e+00 5.92e-01 1.43e+01 angle pdb=" CA LEU A 308 " pdb=" C LEU A 308 " pdb=" N GLU A 309 " ideal model delta sigma weight residual 117.39 121.98 -4.59 1.24e+00 6.50e-01 1.37e+01 angle pdb=" CB HIS A 304 " pdb=" CG HIS A 304 " pdb=" CD2 HIS A 304 " ideal model delta sigma weight residual 131.20 126.42 4.78 1.30e+00 5.92e-01 1.35e+01 angle pdb=" N LEU C 303 " pdb=" CA LEU C 303 " pdb=" CB LEU C 303 " ideal model delta sigma weight residual 110.01 105.16 4.85 1.45e+00 4.76e-01 1.12e+01 ... (remaining 31954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.47: 13987 31.47 - 62.95: 274 62.95 - 94.42: 34 94.42 - 125.90: 0 125.90 - 157.37: 2 Dihedral angle restraints: 14297 sinusoidal: 5467 harmonic: 8830 Sorted by residual: 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 300.00 142.63 157.37 1 2.00e+01 2.50e-03 4.62e+01 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 300.00 170.02 129.98 1 2.00e+01 2.50e-03 3.94e+01 dihedral pdb=" CA GLN E 282 " pdb=" C GLN E 282 " pdb=" N PRO E 283 " pdb=" CA PRO E 283 " ideal model delta harmonic sigma weight residual 180.00 152.29 27.71 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 14294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3228 0.061 - 0.122: 496 0.122 - 0.183: 68 0.183 - 0.243: 7 0.243 - 0.304: 10 Chirality restraints: 3809 Sorted by residual: chirality pdb=" C3' ATP F 600 " pdb=" C2' ATP F 600 " pdb=" C4' ATP F 600 " pdb=" O3' ATP F 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.94 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C3' ATP A 600 " pdb=" C2' ATP A 600 " pdb=" C4' ATP A 600 " pdb=" O3' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.21e+00 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 2.18e+00 ... (remaining 3806 not shown) Planarity restraints: 4113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 302 " -0.049 2.00e-02 2.50e+03 3.49e-02 2.43e+01 pdb=" CG TYR C 302 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR C 302 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR C 302 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR C 302 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR C 302 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYR C 302 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR C 302 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 301 " -0.039 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE C 301 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 301 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE C 301 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE C 301 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE C 301 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 301 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 304 " -0.035 2.00e-02 2.50e+03 2.58e-02 1.00e+01 pdb=" CG HIS C 304 " 0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS C 304 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS C 304 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS C 304 " -0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS C 304 " -0.018 2.00e-02 2.50e+03 ... (remaining 4110 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 33 2.45 - 3.06: 16542 3.06 - 3.67: 33403 3.67 - 4.29: 52710 4.29 - 4.90: 86896 Nonbonded interactions: 189584 Sorted by model distance: nonbonded pdb=" O1G ATP F 600 " pdb="MG MG F 601 " model vdw 1.836 2.170 nonbonded pdb=" O3G ATP B 600 " pdb="MG MG B 601 " model vdw 1.933 2.170 nonbonded pdb=" O1B ATP C 600 " pdb="MG MG C 601 " model vdw 1.933 2.170 nonbonded pdb=" O3B ADP D 600 " pdb="MG MG D 601 " model vdw 1.936 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 1.941 2.170 ... (remaining 189579 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 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 68 or (resid 69 and (name N or nam \ e CA or name C or name O or name CB )) or resid 70 through 145 or (resid 146 and \ (name N or name CA or name C or name O or name CB )) or resid 147 through 155 o \ r (resid 156 through 157 and (name N or name CA or name C or name O or name CB ) \ ) or resid 158 through 166 or (resid 167 and (name N or name CA or name C or nam \ e O or name CB )) or resid 168 through 171 or (resid 172 and (name N or name CA \ or name C or name O or name CB )) or resid 173 through 239 or (resid 240 through \ 242 and (name N or name CA or name C or name O or name CB )) or resid 243 throu \ gh 293 or (resid 294 through 295 and (name N or name CA or name C or name O or n \ ame CB )) or resid 296 through 393 or (resid 394 and (name N or name CA or name \ C or name O or name CB )) or resid 395 through 404 or (resid 405 and (name N or \ name CA or name C or name O or name CB )) or (resid 412 through 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 416 or (resid \ 417 and (name N or name CA or name C or name O or name CB )) or resid 418 throug \ h 430 or (resid 431 and (name N or name CA or name C or name O or name CB )) or \ resid 432 through 453 or (resid 454 through 456 and (name N or name CA or name C \ or name O or name CB )) or resid 457 or (resid 458 through 459 and (name N or n \ ame CA or name C or name O or name CB )) or resid 460 through 464 or (resid 465 \ and (name N or name CA or name C or name O or name CB )) or resid 466 through 47 \ 6 or (resid 477 and (name N or name CA or name C or name O or name CB )) or resi \ d 478 through 509 or resid 600 through 601)) selection = (chain 'B' and (resid 30 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 55 or (resid 56 and (name N or nam \ e CA or name C or name O or name CB )) or resid 57 through 87 or (resid 88 and ( \ name N or name CA or name C or name O or name CB )) or resid 89 through 119 or ( \ resid 120 and (name N or name CA or name C or name O or name CB )) or resid 121 \ through 155 or (resid 156 through 157 and (name N or name CA or name C or name O \ or name CB )) or resid 158 through 166 or (resid 167 and (name N or name CA or \ name C or name O or name CB )) or resid 168 through 171 or (resid 172 and (name \ N or name CA or name C or name O or name CB )) or resid 173 through 256 or (resi \ d 257 and (name N or name CA or name C or name O or name CB )) or resid 258 thro \ ugh 271 or (resid 272 and (name N or name CA or name C or name O or name CB )) o \ r resid 273 through 293 or (resid 294 through 295 and (name N or name CA or name \ C or name O or name CB )) or resid 296 through 298 or (resid 299 and (name N or \ name CA or name C or name O or name CB )) or resid 300 through 315 or (resid 31 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 317 through \ 354 or (resid 355 through 356 and (name N or name CA or name C or name O or name \ CB )) or resid 357 through 404 or (resid 405 through 414 and (name N or name CA \ or name C or name O or name CB )) or resid 415 through 416 or (resid 417 and (n \ ame N or name CA or name C or name O or name CB )) or resid 418 through 430 or ( \ resid 431 and (name N or name CA or name C or name O or name CB )) or resid 432 \ through 453 or (resid 454 through 456 and (name N or name CA or name C or name O \ or name CB )) or resid 457 or (resid 458 through 459 and (name N or name CA or \ name C or name O or name CB )) or resid 460 through 464 or (resid 465 and (name \ N or name CA or name C or name O or name CB )) or resid 466 through 479 or (resi \ d 480 and (name N or name CA or name C or name O or name CB )) or resid 481 thro \ ugh 509 or resid 600 through 601)) selection = (chain 'C' and (resid 30 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 68 or (resid 69 and (name N or nam \ e CA or name C or name O or name CB )) or resid 70 through 119 or (resid 120 and \ (name N or name CA or name C or name O or name CB )) or resid 121 through 145 o \ r (resid 146 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 47 through 239 or (resid 240 through 242 and (name N or name CA or name C or nam \ e O or name CB )) or resid 243 through 256 or (resid 257 and (name N or name CA \ or name C or name O or name CB )) or resid 258 through 271 or (resid 272 and (na \ me N or name CA or name C or name O or name CB )) or resid 273 through 298 or (r \ esid 299 and (name N or name CA or name C or name O or name CB )) or resid 300 t \ hrough 315 or (resid 316 and (name N or name CA or name C or name O or name CB ) \ ) or resid 317 through 393 or (resid 394 and (name N or name CA or name C or nam \ e O or name CB )) or resid 395 through 400 or (resid 401 and (name N or name CA \ or name C or name O or name CB )) or resid 402 through 405 or resid 412 through \ 476 or (resid 477 and (name N or name CA or name C or name O or name CB )) or re \ sid 478 through 509 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 9 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 55 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 67 or (resid 68 and (n \ ame N or name CA or name C or name O or name CB )) or resid 69 through 111 or (r \ esid 112 and (name N or name CA or name C or name O or name CB )) or resid 113 t \ hrough 168 or (resid 169 and (name N or name CA or name C or name O or name CB ) \ ) or resid 170 through 188 or (resid 189 and (name N or name CA or name C or nam \ e O or name CB )) or resid 190 through 192 or (resid 193 and (name N or name CA \ or name C or name O or name CB )) or resid 194 through 202 or (resid 203 and (na \ me N or name CA or name C or name O or name CB )) or resid 204 through 240 or (r \ esid 241 and (name N or name CA or name C or name O or name CB )) or resid 242 t \ hrough 244 or (resid 245 through 246 and (name N or name CA or name C or name O \ or name CB )) or resid 247 through 266 or (resid 267 and (name N or name CA or n \ ame C or name O or name CB )) or resid 268 through 287 or (resid 288 and (name N \ or name CA or name C or name O or name CB )) or resid 289 through 314 or (resid \ 315 and (name N or name CA or name C or name O or name CB )) or resid 316 throu \ gh 336 or (resid 337 and (name N or name CA or name C or name O or name CB )) or \ resid 338 through 341 or (resid 342 and (name N or name CA or name C or name O \ or name CB )) or resid 343 through 358 or (resid 359 through 361 and (name N or \ name CA or name C or name O or name CB )) or resid 362 through 381 or (resid 382 \ and (name N or name CA or name C or name O or name CB )) or resid 383 or (resid \ 384 through 391 and (name N or name CA or name C or name O or name CB )) or res \ id 392 or (resid 393 through 402 and (name N or name CA or name C or name O or n \ ame CB )) or resid 403 through 408 or (resid 409 and (name N or name CA or name \ C or name O or name CB )) or resid 410 through 421 or (resid 422 and (name N or \ name CA or name C or name O or name CB )) or resid 423 through 429 or (resid 430 \ and (name N or name CA or name C or name O or name CB )) or resid 431 through 4 \ 75)) selection = (chain 'E' and (resid 9 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 67 or (resid 68 and (name N or name \ CA or name C or name O or name CB )) or resid 69 through 111 or (resid 112 and \ (name N or name CA or name C or name O or name CB )) or resid 113 through 188 or \ (resid 189 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 0 through 192 or (resid 193 and (name N or name CA or name C or name O or name C \ B )) or resid 194 through 195 or (resid 196 and (name N or name CA or name C or \ name O or name CB )) or resid 197 through 209 or (resid 210 and (name N or name \ CA or name C or name O or name CB )) or resid 211 or (resid 212 and (name N or n \ ame CA or name C or name O or name CB )) or resid 213 through 266 or (resid 267 \ and (name N or name CA or name C or name O or name CB )) or resid 268 through 29 \ 9 or (resid 300 and (name N or name CA or name C or name O or name CB )) or resi \ d 301 through 358 or (resid 359 through 361 and (name N or name CA or name C or \ name O or name CB )) or resid 362 through 429 or (resid 430 and (name N or name \ CA or name C or name O or name CB )) or resid 431 through 471 or (resid 472 and \ (name N or name CA or name C or name O or name CB )) or resid 473 through 475)) selection = (chain 'F' and (resid 9 through 25 or (resid 26 through 27 and (name N or name C \ A or name C or name O or name CB )) or resid 28 or (resid 29 and (name N or name \ CA or name C or name O or name CB )) or resid 30 through 42 or (resid 43 and (n \ ame N or name CA or name C or name O or name CB )) or resid 44 through 64 or (re \ sid 65 and (name N or name CA or name C or name O or name CB )) or resid 66 thro \ ugh 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) o \ r resid 170 through 195 or (resid 196 and (name N or name CA or name C or name O \ or name CB )) or resid 197 through 202 or (resid 203 and (name N or name CA or \ name C or name O or name CB )) or resid 204 through 211 or (resid 212 and (name \ N or name CA or name C or name O or name CB )) or resid 213 through 240 or (resi \ d 241 and (name N or name CA or name C or name O or name CB )) or resid 242 thro \ ugh 244 or (resid 245 through 246 and (name N or name CA or name C or name O or \ name CB )) or resid 247 through 287 or (resid 288 and (name N or name CA or name \ C or name O or name CB )) or resid 289 through 299 or (resid 300 and (name N or \ name CA or name C or name O or name CB )) or resid 301 through 314 or (resid 31 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 316 through \ 336 or (resid 337 and (name N or name CA or name C or name O or name CB )) or re \ sid 338 through 340 or (resid 341 through 342 and (name N or name CA or name C o \ r name O or name CB )) or resid 343 through 375 or (resid 376 and (name N or nam \ e CA or name C or name O or name CB )) or resid 377 through 381 or (resid 382 an \ d (name N or name CA or name C or name O or name CB )) or resid 383 or (resid 38 \ 4 through 391 and (name N or name CA or name C or name O or name CB )) or resid \ 392 or (resid 393 through 402 and (name N or name CA or name C or name O or name \ CB )) or resid 403 through 404 or (resid 405 and (name N or name CA or name C o \ r name O or name CB )) or resid 406 through 408 or (resid 409 and (name N or nam \ e CA or name C or name O or name CB )) or resid 410 through 421 or (resid 422 an \ d (name N or name CA or name C or name O or name CB )) or resid 423 through 445 \ or (resid 446 and (name N or name CA or name C or name O or name CB )) or resid \ 447 through 463 or (resid 464 through 465 and (name N or name CA or name C or na \ me O or name CB )) or resid 466 through 470 or (resid 471 through 472 and (name \ N or name CA or name C or name O or name CB )) or resid 473 through 475)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.940 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 63.240 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 0.078 23527 Z= 0.207 Angle : 0.663 6.914 31959 Z= 0.371 Chirality : 0.047 0.304 3809 Planarity : 0.005 0.076 4113 Dihedral : 12.839 157.371 8647 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: 0.21 (0.15), residues: 3092 helix: 0.32 (0.14), residues: 1254 sheet: 0.03 (0.23), residues: 471 loop : 0.22 (0.18), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.006 0.001 HIS D 367 PHE 0.039 0.002 PHE C 301 TYR 0.062 0.002 TYR C 302 ARG 0.007 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 955 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8011 (mp0) cc_final: 0.7713 (mp0) REVERT: A 62 LYS cc_start: 0.8666 (mttp) cc_final: 0.8205 (mtmm) REVERT: A 228 MET cc_start: 0.8159 (tpt) cc_final: 0.7529 (tpt) REVERT: A 302 TYR cc_start: 0.8934 (t80) cc_final: 0.8521 (t80) REVERT: A 342 THR cc_start: 0.8926 (m) cc_final: 0.8460 (p) REVERT: A 436 SER cc_start: 0.8368 (m) cc_final: 0.7926 (t) REVERT: A 462 ARG cc_start: 0.8036 (ttm170) cc_final: 0.6060 (ttt180) REVERT: B 56 GLU cc_start: 0.7391 (tt0) cc_final: 0.7124 (tt0) REVERT: B 124 ASP cc_start: 0.7000 (t0) cc_final: 0.6795 (t70) REVERT: B 165 GLN cc_start: 0.8086 (tt0) cc_final: 0.7824 (tt0) REVERT: B 189 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8089 (pttm) REVERT: B 226 ASP cc_start: 0.9008 (t0) cc_final: 0.8646 (t70) REVERT: B 247 LEU cc_start: 0.8860 (tp) cc_final: 0.8485 (tp) REVERT: B 257 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7270 (mt-10) REVERT: B 337 SER cc_start: 0.8760 (m) cc_final: 0.8528 (p) REVERT: B 486 ARG cc_start: 0.7867 (ttm170) cc_final: 0.7140 (ttm-80) REVERT: C 64 MET cc_start: 0.8711 (ttt) cc_final: 0.8216 (ttm) REVERT: C 91 LYS cc_start: 0.8665 (mttt) cc_final: 0.8445 (mttm) REVERT: C 113 LEU cc_start: 0.9198 (mt) cc_final: 0.8845 (tp) REVERT: C 493 LYS cc_start: 0.7775 (mttt) cc_final: 0.7424 (mmmt) REVERT: D 38 GLU cc_start: 0.7650 (pt0) cc_final: 0.7327 (mt-10) REVERT: D 167 ILE cc_start: 0.9186 (mt) cc_final: 0.8822 (mt) REVERT: D 169 GLU cc_start: 0.7653 (tp30) cc_final: 0.7323 (tp30) REVERT: D 369 ASP cc_start: 0.7578 (m-30) cc_final: 0.7315 (m-30) REVERT: D 386 ASP cc_start: 0.7874 (m-30) cc_final: 0.7623 (m-30) REVERT: E 65 ASP cc_start: 0.8403 (t0) cc_final: 0.8124 (t0) REVERT: E 75 LYS cc_start: 0.7935 (ttpt) cc_final: 0.7605 (ttpp) REVERT: E 101 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7539 (mm-30) REVERT: E 113 LEU cc_start: 0.7895 (mp) cc_final: 0.7611 (mt) REVERT: E 224 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8262 (mm-30) REVERT: E 262 THR cc_start: 0.8908 (m) cc_final: 0.8524 (m) REVERT: E 266 SER cc_start: 0.9340 (t) cc_final: 0.9099 (t) REVERT: E 282 GLN cc_start: 0.8927 (pt0) cc_final: 0.8614 (pt0) REVERT: E 354 LYS cc_start: 0.7861 (tttt) cc_final: 0.7265 (ttmm) REVERT: E 373 LYS cc_start: 0.8321 (mttm) cc_final: 0.7996 (mtpt) REVERT: F 84 SER cc_start: 0.8941 (m) cc_final: 0.8686 (p) REVERT: F 123 SER cc_start: 0.8727 (p) cc_final: 0.8225 (t) REVERT: F 126 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7454 (mm-30) REVERT: F 161 VAL cc_start: 0.9376 (m) cc_final: 0.9155 (p) REVERT: F 235 THR cc_start: 0.8658 (m) cc_final: 0.8445 (m) REVERT: F 237 LEU cc_start: 0.8277 (mp) cc_final: 0.8066 (mp) REVERT: F 241 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7687 (tt0) REVERT: F 336 SER cc_start: 0.9163 (t) cc_final: 0.8652 (p) REVERT: G 101 ASP cc_start: 0.7427 (m-30) cc_final: 0.6794 (m-30) REVERT: G 218 MET cc_start: 0.8162 (ttp) cc_final: 0.7881 (ttp) outliers start: 0 outliers final: 0 residues processed: 955 average time/residue: 0.3462 time to fit residues: 507.5279 Evaluate side-chains 727 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 727 time to evaluate : 2.551 ------------------------------------------------------------------------------- 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: 0.9980 chunk 232 optimal weight: 0.8980 chunk 129 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 0.3980 chunk 124 optimal weight: 5.9990 chunk 240 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 chunk 146 optimal weight: 0.0980 chunk 179 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 192 ASN B 381 GLN ** B 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS C 282 GLN C 478 HIS D 263 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN E 379 GLN F 178 HIS F 293 GLN F 308 GLN G 90 GLN G 265 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 23527 Z= 0.162 Angle : 0.569 10.547 31959 Z= 0.292 Chirality : 0.044 0.169 3809 Planarity : 0.004 0.048 4113 Dihedral : 7.843 168.464 3486 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.99 % Allowed : 11.11 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: 0.74 (0.15), residues: 3092 helix: 0.88 (0.15), residues: 1252 sheet: 0.22 (0.23), residues: 483 loop : 0.42 (0.18), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 258 HIS 0.006 0.001 HIS B 478 PHE 0.021 0.001 PHE F 261 TYR 0.019 0.001 TYR D 458 ARG 0.006 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 782 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8014 (mp0) cc_final: 0.7763 (mp0) REVERT: A 62 LYS cc_start: 0.8724 (mttp) cc_final: 0.8334 (mtmm) REVERT: A 228 MET cc_start: 0.8230 (tpt) cc_final: 0.7573 (tpt) REVERT: A 302 TYR cc_start: 0.8953 (t80) cc_final: 0.8674 (t80) REVERT: A 436 SER cc_start: 0.8414 (m) cc_final: 0.7879 (t) REVERT: A 462 ARG cc_start: 0.8126 (ttm170) cc_final: 0.5893 (ttt180) REVERT: B 124 ASP cc_start: 0.6927 (t0) cc_final: 0.6695 (t70) REVERT: B 169 ILE cc_start: 0.7871 (mt) cc_final: 0.7571 (mp) REVERT: B 189 LYS cc_start: 0.8483 (ttpp) cc_final: 0.7943 (pttm) REVERT: B 206 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8608 (m) REVERT: B 226 ASP cc_start: 0.9039 (t0) cc_final: 0.8553 (t0) REVERT: B 247 LEU cc_start: 0.8609 (tp) cc_final: 0.8217 (tp) REVERT: B 257 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7004 (mt-10) REVERT: B 306 ARG cc_start: 0.8489 (ptt-90) cc_final: 0.8239 (ptt-90) REVERT: B 313 LYS cc_start: 0.8372 (tttt) cc_final: 0.8167 (tttt) REVERT: B 336 VAL cc_start: 0.9005 (m) cc_final: 0.8587 (t) REVERT: B 337 SER cc_start: 0.8961 (m) cc_final: 0.8560 (p) REVERT: B 486 ARG cc_start: 0.7830 (ttm170) cc_final: 0.7264 (ttm-80) REVERT: C 64 MET cc_start: 0.8692 (ttt) cc_final: 0.8306 (ttt) REVERT: C 91 LYS cc_start: 0.8670 (mttt) cc_final: 0.8458 (mttm) REVERT: C 257 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8189 (mt-10) REVERT: C 357 GLU cc_start: 0.7798 (tt0) cc_final: 0.7569 (tt0) REVERT: C 493 LYS cc_start: 0.7611 (mttt) cc_final: 0.7307 (mmmt) REVERT: D 38 GLU cc_start: 0.7594 (pt0) cc_final: 0.7308 (mt-10) REVERT: D 200 GLU cc_start: 0.8314 (tp30) cc_final: 0.8108 (tp30) REVERT: D 258 ILE cc_start: 0.8110 (tp) cc_final: 0.7887 (tp) REVERT: D 369 ASP cc_start: 0.7672 (m-30) cc_final: 0.7278 (m-30) REVERT: D 401 LYS cc_start: 0.7236 (mtpp) cc_final: 0.6940 (mtmm) REVERT: E 75 LYS cc_start: 0.7806 (ttpt) cc_final: 0.7499 (ttpp) REVERT: E 90 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7621 (mm-30) REVERT: E 101 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7576 (mm-30) REVERT: E 168 GLN cc_start: 0.7815 (mt0) cc_final: 0.7561 (mt0) REVERT: E 201 MET cc_start: 0.7849 (mtt) cc_final: 0.7599 (mtt) REVERT: E 282 GLN cc_start: 0.8867 (pt0) cc_final: 0.8606 (pt0) REVERT: E 326 PHE cc_start: 0.8406 (m-10) cc_final: 0.8115 (m-10) REVERT: E 354 LYS cc_start: 0.7762 (tttt) cc_final: 0.7334 (mtpp) REVERT: E 373 LYS cc_start: 0.8325 (mttm) cc_final: 0.7971 (mtpt) REVERT: E 430 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7834 (mmtp) REVERT: F 38 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7858 (mt-10) REVERT: F 84 SER cc_start: 0.8843 (m) cc_final: 0.8525 (p) REVERT: F 126 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7628 (mm-30) REVERT: F 218 VAL cc_start: 0.8937 (t) cc_final: 0.8708 (m) REVERT: F 241 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7616 (tt0) REVERT: F 243 PHE cc_start: 0.8342 (m-80) cc_final: 0.7864 (m-80) REVERT: F 292 LEU cc_start: 0.8954 (tp) cc_final: 0.8512 (tp) REVERT: G 18 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7550 (ttpp) REVERT: G 45 ASP cc_start: 0.8598 (t0) cc_final: 0.8341 (t0) REVERT: G 242 LYS cc_start: 0.8632 (tppt) cc_final: 0.8178 (ttpt) outliers start: 47 outliers final: 30 residues processed: 797 average time/residue: 0.3440 time to fit residues: 426.2826 Evaluate side-chains 733 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 702 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 154 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 279 optimal weight: 3.9990 chunk 301 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN B 174 GLN B 192 ASN B 443 GLN C 478 HIS D 127 GLN D 308 GLN D 399 GLN E 52 GLN F 178 HIS F 308 GLN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 23527 Z= 0.381 Angle : 0.637 11.146 31959 Z= 0.325 Chirality : 0.047 0.246 3809 Planarity : 0.005 0.042 4113 Dihedral : 8.074 176.817 3486 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.16 % Allowed : 14.21 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: 0.35 (0.15), residues: 3092 helix: 0.72 (0.15), residues: 1246 sheet: -0.02 (0.23), residues: 488 loop : 0.05 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 258 HIS 0.007 0.001 HIS A 478 PHE 0.018 0.002 PHE F 261 TYR 0.017 0.002 TYR B 246 ARG 0.006 0.001 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 690 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8272 (tpt) cc_final: 0.7736 (tpt) REVERT: A 276 GLN cc_start: 0.8297 (tt0) cc_final: 0.7939 (tt0) REVERT: A 302 TYR cc_start: 0.8994 (t80) cc_final: 0.8660 (t80) REVERT: A 421 VAL cc_start: 0.8189 (t) cc_final: 0.7896 (p) REVERT: A 436 SER cc_start: 0.8565 (m) cc_final: 0.8056 (t) REVERT: B 165 GLN cc_start: 0.8194 (tt0) cc_final: 0.7913 (tt0) REVERT: B 189 LYS cc_start: 0.8645 (ttpp) cc_final: 0.8120 (pttm) REVERT: B 226 ASP cc_start: 0.9082 (t70) cc_final: 0.8495 (t0) REVERT: B 247 LEU cc_start: 0.8480 (tp) cc_final: 0.8060 (tp) REVERT: B 306 ARG cc_start: 0.8469 (ptt-90) cc_final: 0.8223 (ptt-90) REVERT: B 337 SER cc_start: 0.9193 (m) cc_final: 0.8693 (p) REVERT: B 418 GLN cc_start: 0.5797 (mp10) cc_final: 0.5382 (mp10) REVERT: B 480 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8555 (mp0) REVERT: B 486 ARG cc_start: 0.8101 (ttm170) cc_final: 0.7507 (ttm-80) REVERT: C 53 GLU cc_start: 0.8197 (tt0) cc_final: 0.7983 (tt0) REVERT: C 64 MET cc_start: 0.8837 (ttt) cc_final: 0.8357 (ttt) REVERT: C 91 LYS cc_start: 0.8709 (mttt) cc_final: 0.8460 (mttm) REVERT: C 197 GLU cc_start: 0.7211 (tt0) cc_final: 0.7000 (mp0) REVERT: C 276 GLN cc_start: 0.8705 (tt0) cc_final: 0.8390 (tt0) REVERT: C 441 GLU cc_start: 0.8147 (pt0) cc_final: 0.7930 (pt0) REVERT: C 493 LYS cc_start: 0.7513 (mttt) cc_final: 0.7290 (mmmt) REVERT: D 38 GLU cc_start: 0.7629 (pt0) cc_final: 0.7337 (mt-10) REVERT: D 258 ILE cc_start: 0.8256 (tp) cc_final: 0.8044 (tp) REVERT: D 352 ASP cc_start: 0.8619 (t0) cc_final: 0.8397 (t0) REVERT: D 401 LYS cc_start: 0.7283 (mtpp) cc_final: 0.6907 (mtmm) REVERT: D 406 ARG cc_start: 0.7565 (mtt180) cc_final: 0.6983 (mtm-85) REVERT: E 75 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7706 (ttpp) REVERT: E 135 GLU cc_start: 0.8442 (mp0) cc_final: 0.7985 (mp0) REVERT: E 136 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8840 (t) REVERT: E 262 THR cc_start: 0.8923 (m) cc_final: 0.8720 (m) REVERT: E 282 GLN cc_start: 0.9007 (pt0) cc_final: 0.8706 (pt0) REVERT: E 356 ARG cc_start: 0.8469 (tpp80) cc_final: 0.8234 (ttm170) REVERT: E 373 LYS cc_start: 0.8429 (mttm) cc_final: 0.8063 (mtpt) REVERT: F 38 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7933 (mt-10) REVERT: F 84 SER cc_start: 0.8795 (m) cc_final: 0.8397 (p) REVERT: F 126 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7443 (mm-30) REVERT: F 161 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9125 (p) REVERT: F 218 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8734 (m) REVERT: F 241 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7643 (tt0) REVERT: F 243 PHE cc_start: 0.8426 (m-80) cc_final: 0.8128 (m-80) REVERT: G 18 LYS cc_start: 0.7889 (ttmm) cc_final: 0.7510 (ttpp) REVERT: G 218 MET cc_start: 0.7802 (ttm) cc_final: 0.7410 (ttm) REVERT: G 242 LYS cc_start: 0.8679 (tppt) cc_final: 0.8138 (ttpt) outliers start: 98 outliers final: 74 residues processed: 729 average time/residue: 0.3420 time to fit residues: 390.8464 Evaluate side-chains 747 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 669 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 275 optimal weight: 0.6980 chunk 209 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 133 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 280 optimal weight: 0.0170 chunk 296 optimal weight: 4.9990 chunk 146 optimal weight: 0.0030 chunk 265 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN D 223 ASN D 308 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23527 Z= 0.138 Angle : 0.523 10.551 31959 Z= 0.266 Chirality : 0.043 0.270 3809 Planarity : 0.004 0.041 4113 Dihedral : 7.430 176.327 3486 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.63 % Allowed : 17.94 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: 0.66 (0.15), residues: 3092 helix: 0.98 (0.15), residues: 1262 sheet: 0.21 (0.23), residues: 495 loop : 0.16 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 258 HIS 0.004 0.001 HIS A 145 PHE 0.018 0.001 PHE F 261 TYR 0.015 0.001 TYR E 458 ARG 0.005 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 713 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7254 (ttt90) cc_final: 0.6739 (ttt90) REVERT: A 228 MET cc_start: 0.8255 (tpt) cc_final: 0.7740 (tpt) REVERT: A 276 GLN cc_start: 0.8168 (tt0) cc_final: 0.7756 (tt0) REVERT: A 302 TYR cc_start: 0.9000 (t80) cc_final: 0.8607 (t80) REVERT: A 436 SER cc_start: 0.8451 (m) cc_final: 0.7994 (t) REVERT: B 96 ILE cc_start: 0.9009 (mm) cc_final: 0.8788 (mm) REVERT: B 189 LYS cc_start: 0.8434 (ttpp) cc_final: 0.8020 (pttm) REVERT: B 226 ASP cc_start: 0.9020 (t70) cc_final: 0.8463 (t0) REVERT: B 247 LEU cc_start: 0.8427 (tp) cc_final: 0.7999 (tp) REVERT: B 306 ARG cc_start: 0.8353 (ptt-90) cc_final: 0.8130 (ptt-90) REVERT: B 336 VAL cc_start: 0.9152 (m) cc_final: 0.8821 (t) REVERT: B 337 SER cc_start: 0.8989 (m) cc_final: 0.8490 (p) REVERT: B 480 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: B 486 ARG cc_start: 0.7982 (ttm170) cc_final: 0.7350 (ttm-80) REVERT: C 53 GLU cc_start: 0.8065 (tt0) cc_final: 0.7855 (tt0) REVERT: C 56 GLU cc_start: 0.7492 (tt0) cc_final: 0.7017 (tm-30) REVERT: C 64 MET cc_start: 0.8779 (ttt) cc_final: 0.8315 (ttt) REVERT: C 197 GLU cc_start: 0.6958 (tt0) cc_final: 0.6724 (mp0) REVERT: C 441 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7786 (pt0) REVERT: C 493 LYS cc_start: 0.7507 (mttt) cc_final: 0.7290 (mmmt) REVERT: D 262 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8382 (p) REVERT: D 393 MET cc_start: 0.7608 (tpt) cc_final: 0.6909 (tpp) REVERT: D 401 LYS cc_start: 0.7341 (mtpp) cc_final: 0.6920 (mtmm) REVERT: D 406 ARG cc_start: 0.7535 (mtt180) cc_final: 0.6989 (mtm-85) REVERT: D 412 ARG cc_start: 0.8514 (mtt90) cc_final: 0.8167 (mmt-90) REVERT: E 75 LYS cc_start: 0.7959 (ttpt) cc_final: 0.7599 (ttpp) REVERT: E 135 GLU cc_start: 0.8430 (mp0) cc_final: 0.8152 (mp0) REVERT: E 282 GLN cc_start: 0.8742 (pt0) cc_final: 0.8488 (pt0) REVERT: E 373 LYS cc_start: 0.8553 (mttm) cc_final: 0.8105 (mtpt) REVERT: F 38 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7836 (mt-10) REVERT: F 126 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7485 (mm-30) REVERT: F 237 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8289 (mp) REVERT: F 241 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7575 (tt0) REVERT: F 300 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7843 (mttp) REVERT: G 18 LYS cc_start: 0.7852 (ttmm) cc_final: 0.7467 (ttpp) REVERT: G 218 MET cc_start: 0.7789 (ttm) cc_final: 0.7375 (ttm) REVERT: G 242 LYS cc_start: 0.8643 (tppt) cc_final: 0.8122 (ttpt) REVERT: G 254 LEU cc_start: 0.8852 (tp) cc_final: 0.8650 (tp) REVERT: G 265 ASN cc_start: 0.8993 (m-40) cc_final: 0.8597 (m110) outliers start: 62 outliers final: 42 residues processed: 737 average time/residue: 0.3428 time to fit residues: 394.7525 Evaluate side-chains 717 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 671 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 247 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 4 optimal weight: 0.0020 chunk 220 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 253 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 151 optimal weight: 0.4980 chunk 266 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN A 452 ASN C 192 ASN E 127 GLN E 411 GLN F 118 HIS ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN G 217 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23527 Z= 0.247 Angle : 0.553 10.841 31959 Z= 0.279 Chirality : 0.044 0.289 3809 Planarity : 0.004 0.042 4113 Dihedral : 7.382 176.078 3486 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.86 % Allowed : 18.70 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: 0.60 (0.15), residues: 3092 helix: 0.98 (0.15), residues: 1260 sheet: 0.22 (0.24), residues: 474 loop : 0.05 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 258 HIS 0.004 0.001 HIS A 478 PHE 0.019 0.001 PHE F 261 TYR 0.028 0.001 TYR E 458 ARG 0.007 0.000 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 689 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8644 (tp) cc_final: 0.8303 (tp) REVERT: A 228 MET cc_start: 0.8277 (tpt) cc_final: 0.7795 (tpt) REVERT: A 276 GLN cc_start: 0.8207 (tt0) cc_final: 0.7808 (tt0) REVERT: A 302 TYR cc_start: 0.8935 (t80) cc_final: 0.8609 (t80) REVERT: A 436 SER cc_start: 0.8546 (m) cc_final: 0.8107 (t) REVERT: B 189 LYS cc_start: 0.8579 (ttpp) cc_final: 0.7961 (pttp) REVERT: B 226 ASP cc_start: 0.9053 (t70) cc_final: 0.8479 (t0) REVERT: B 257 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7221 (mt-10) REVERT: B 336 VAL cc_start: 0.9220 (m) cc_final: 0.8898 (t) REVERT: B 337 SER cc_start: 0.9179 (m) cc_final: 0.8656 (p) REVERT: B 418 GLN cc_start: 0.5738 (OUTLIER) cc_final: 0.5450 (mp10) REVERT: B 486 ARG cc_start: 0.8112 (ttm170) cc_final: 0.7421 (ttm-80) REVERT: C 53 GLU cc_start: 0.8156 (tt0) cc_final: 0.7943 (tt0) REVERT: C 56 GLU cc_start: 0.7610 (tt0) cc_final: 0.7075 (tm-30) REVERT: C 64 MET cc_start: 0.8811 (ttt) cc_final: 0.8350 (ttt) REVERT: C 141 ARG cc_start: 0.8002 (mtt90) cc_final: 0.7189 (mtt90) REVERT: C 208 VAL cc_start: 0.9048 (t) cc_final: 0.8689 (m) REVERT: C 493 LYS cc_start: 0.7467 (mttt) cc_final: 0.7229 (mmmt) REVERT: D 393 MET cc_start: 0.7692 (tpt) cc_final: 0.6908 (tpp) REVERT: D 401 LYS cc_start: 0.7385 (mtpp) cc_final: 0.6992 (mtmm) REVERT: E 75 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7668 (ttpp) REVERT: E 135 GLU cc_start: 0.8447 (mp0) cc_final: 0.8055 (mp0) REVERT: E 282 GLN cc_start: 0.8776 (pt0) cc_final: 0.8513 (pt0) REVERT: E 373 LYS cc_start: 0.8535 (mttm) cc_final: 0.8225 (mtpt) REVERT: F 126 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7403 (mm-30) REVERT: F 241 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7485 (tt0) REVERT: F 261 PHE cc_start: 0.8407 (t80) cc_final: 0.8094 (t80) REVERT: F 300 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7848 (mttp) REVERT: G 18 LYS cc_start: 0.7826 (ttmm) cc_final: 0.7440 (ttpp) REVERT: G 180 LYS cc_start: 0.6320 (pttt) cc_final: 0.5992 (pttm) REVERT: G 218 MET cc_start: 0.7831 (ttm) cc_final: 0.7368 (ttm) REVERT: G 242 LYS cc_start: 0.8634 (tppt) cc_final: 0.8120 (ttpt) REVERT: G 254 LEU cc_start: 0.8886 (tp) cc_final: 0.8655 (tp) REVERT: G 265 ASN cc_start: 0.9004 (m-40) cc_final: 0.8617 (m110) outliers start: 91 outliers final: 71 residues processed: 726 average time/residue: 0.3328 time to fit residues: 378.4355 Evaluate side-chains 751 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 678 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 99 optimal weight: 0.9990 chunk 267 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 297 optimal weight: 4.9990 chunk 246 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 155 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN D 308 GLN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23527 Z= 0.185 Angle : 0.530 10.912 31959 Z= 0.267 Chirality : 0.044 0.298 3809 Planarity : 0.004 0.043 4113 Dihedral : 7.165 174.889 3486 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.35 % Allowed : 19.59 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: 0.69 (0.15), residues: 3092 helix: 1.06 (0.15), residues: 1263 sheet: 0.33 (0.24), residues: 466 loop : 0.07 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 258 HIS 0.003 0.001 HIS G 88 PHE 0.017 0.001 PHE F 261 TYR 0.019 0.001 TYR E 458 ARG 0.008 0.000 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 693 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8163 (tpt) cc_final: 0.7697 (tpt) REVERT: A 276 GLN cc_start: 0.8185 (tt0) cc_final: 0.7751 (tt0) REVERT: A 302 TYR cc_start: 0.8926 (t80) cc_final: 0.8692 (t80) REVERT: A 436 SER cc_start: 0.8501 (m) cc_final: 0.8053 (t) REVERT: B 189 LYS cc_start: 0.8591 (ttpp) cc_final: 0.7922 (pttp) REVERT: B 226 ASP cc_start: 0.9039 (t70) cc_final: 0.8503 (t0) REVERT: B 257 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7182 (mt-10) REVERT: B 336 VAL cc_start: 0.9219 (m) cc_final: 0.8941 (t) REVERT: B 337 SER cc_start: 0.8916 (m) cc_final: 0.8363 (p) REVERT: B 418 GLN cc_start: 0.5766 (OUTLIER) cc_final: 0.5493 (mp10) REVERT: B 480 GLU cc_start: 0.8557 (mp0) cc_final: 0.8339 (mp0) REVERT: B 486 ARG cc_start: 0.8126 (ttm170) cc_final: 0.7386 (ttm-80) REVERT: C 56 GLU cc_start: 0.7567 (tt0) cc_final: 0.7062 (tm-30) REVERT: C 64 MET cc_start: 0.8750 (ttt) cc_final: 0.8302 (ttt) REVERT: C 141 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7332 (mtt90) REVERT: C 208 VAL cc_start: 0.9048 (t) cc_final: 0.8714 (m) REVERT: D 393 MET cc_start: 0.7730 (tpt) cc_final: 0.6880 (tpp) REVERT: D 401 LYS cc_start: 0.7401 (mtpp) cc_final: 0.7000 (mtmm) REVERT: D 412 ARG cc_start: 0.8525 (mtt90) cc_final: 0.8225 (mmt-90) REVERT: E 75 LYS cc_start: 0.7997 (ttpt) cc_final: 0.7679 (ttpp) REVERT: E 135 GLU cc_start: 0.8437 (mp0) cc_final: 0.8104 (mp0) REVERT: E 192 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7685 (ptm-80) REVERT: E 282 GLN cc_start: 0.8714 (pt0) cc_final: 0.8469 (pt0) REVERT: E 373 LYS cc_start: 0.8531 (mttm) cc_final: 0.8202 (mtpt) REVERT: F 126 GLU cc_start: 0.7791 (mt-10) cc_final: 0.6916 (mt-10) REVERT: F 214 LYS cc_start: 0.8563 (pttm) cc_final: 0.8172 (pttp) REVERT: F 237 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8312 (mp) REVERT: F 241 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7595 (tt0) REVERT: F 300 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7876 (mttp) REVERT: F 325 THR cc_start: 0.9006 (m) cc_final: 0.8601 (p) REVERT: G 18 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7549 (ttpp) REVERT: G 218 MET cc_start: 0.8012 (ttm) cc_final: 0.7534 (ttm) REVERT: G 242 LYS cc_start: 0.8616 (tppt) cc_final: 0.8114 (ttpt) REVERT: G 254 LEU cc_start: 0.8826 (tp) cc_final: 0.8607 (tp) REVERT: G 265 ASN cc_start: 0.8974 (m-40) cc_final: 0.8566 (m110) outliers start: 79 outliers final: 65 residues processed: 722 average time/residue: 0.3388 time to fit residues: 380.6744 Evaluate side-chains 737 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 669 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 286 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 216 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 295 optimal weight: 0.0670 chunk 185 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN D 308 GLN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23527 Z= 0.177 Angle : 0.530 11.381 31959 Z= 0.268 Chirality : 0.043 0.323 3809 Planarity : 0.004 0.044 4113 Dihedral : 7.042 171.717 3486 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.69 % Allowed : 20.44 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: 0.71 (0.15), residues: 3092 helix: 1.10 (0.15), residues: 1271 sheet: 0.34 (0.24), residues: 465 loop : 0.06 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 258 HIS 0.007 0.001 HIS A 145 PHE 0.020 0.001 PHE B 506 TYR 0.029 0.001 TYR E 458 ARG 0.008 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 669 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8631 (tp) cc_final: 0.8302 (tp) REVERT: A 228 MET cc_start: 0.8143 (tpt) cc_final: 0.7692 (tpt) REVERT: A 436 SER cc_start: 0.8484 (m) cc_final: 0.8073 (t) REVERT: B 91 LYS cc_start: 0.8439 (mmmm) cc_final: 0.8133 (mmmt) REVERT: B 189 LYS cc_start: 0.8501 (ttpp) cc_final: 0.7881 (pttp) REVERT: B 226 ASP cc_start: 0.9027 (t70) cc_final: 0.8516 (t0) REVERT: B 257 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7151 (mt-10) REVERT: B 336 VAL cc_start: 0.9243 (m) cc_final: 0.8985 (t) REVERT: B 337 SER cc_start: 0.8906 (m) cc_final: 0.8350 (p) REVERT: B 418 GLN cc_start: 0.5781 (OUTLIER) cc_final: 0.5475 (mp10) REVERT: B 480 GLU cc_start: 0.8446 (mp0) cc_final: 0.8219 (mp0) REVERT: B 486 ARG cc_start: 0.8259 (ttm170) cc_final: 0.7596 (ttm-80) REVERT: C 56 GLU cc_start: 0.7516 (tt0) cc_final: 0.7036 (tm-30) REVERT: C 64 MET cc_start: 0.8742 (ttt) cc_final: 0.8300 (ttt) REVERT: C 141 ARG cc_start: 0.8057 (mtt90) cc_final: 0.7383 (mtt90) REVERT: C 208 VAL cc_start: 0.9036 (t) cc_final: 0.8680 (m) REVERT: C 305 SER cc_start: 0.8739 (p) cc_final: 0.8505 (p) REVERT: D 105 GLU cc_start: 0.7981 (mp0) cc_final: 0.7249 (mp0) REVERT: D 393 MET cc_start: 0.7788 (tpt) cc_final: 0.6904 (tpp) REVERT: D 401 LYS cc_start: 0.7373 (mtpp) cc_final: 0.6972 (mtmm) REVERT: E 68 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6185 (mm-30) REVERT: E 75 LYS cc_start: 0.8001 (ttpt) cc_final: 0.7681 (ttpp) REVERT: E 135 GLU cc_start: 0.8436 (mp0) cc_final: 0.8106 (mp0) REVERT: E 192 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7689 (ptm-80) REVERT: E 282 GLN cc_start: 0.8692 (pt0) cc_final: 0.8459 (pt0) REVERT: E 373 LYS cc_start: 0.8528 (mttm) cc_final: 0.8201 (mtpp) REVERT: F 126 GLU cc_start: 0.7785 (mt-10) cc_final: 0.6912 (mt-10) REVERT: F 214 LYS cc_start: 0.8525 (pttm) cc_final: 0.8291 (pttp) REVERT: F 237 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8331 (mp) REVERT: F 241 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7587 (tt0) REVERT: F 261 PHE cc_start: 0.8296 (t80) cc_final: 0.8030 (t80) REVERT: F 300 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7876 (mttp) REVERT: F 325 THR cc_start: 0.9007 (m) cc_final: 0.8611 (p) REVERT: G 18 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7553 (ttpp) REVERT: G 33 LYS cc_start: 0.8054 (mttm) cc_final: 0.7459 (tttm) REVERT: G 218 MET cc_start: 0.8029 (ttm) cc_final: 0.7581 (ttm) REVERT: G 242 LYS cc_start: 0.8616 (tppt) cc_final: 0.8111 (ttpt) REVERT: G 254 LEU cc_start: 0.8822 (tp) cc_final: 0.8602 (tp) outliers start: 87 outliers final: 69 residues processed: 708 average time/residue: 0.3379 time to fit residues: 374.0844 Evaluate side-chains 715 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 643 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 183 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 176 optimal weight: 0.0870 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 146 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 187 ASN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23527 Z= 0.187 Angle : 0.535 11.676 31959 Z= 0.270 Chirality : 0.044 0.319 3809 Planarity : 0.004 0.044 4113 Dihedral : 6.927 169.144 3486 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.56 % Allowed : 20.70 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: 0.72 (0.15), residues: 3092 helix: 1.11 (0.15), residues: 1271 sheet: 0.29 (0.24), residues: 477 loop : 0.08 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 258 HIS 0.004 0.001 HIS A 145 PHE 0.016 0.001 PHE F 261 TYR 0.024 0.001 TYR E 458 ARG 0.009 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 653 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8161 (tpt) cc_final: 0.7646 (tpt) REVERT: A 436 SER cc_start: 0.8509 (m) cc_final: 0.8106 (t) REVERT: A 465 GLU cc_start: 0.7607 (pt0) cc_final: 0.7313 (pt0) REVERT: B 91 LYS cc_start: 0.8503 (mmmm) cc_final: 0.8199 (mmmt) REVERT: B 189 LYS cc_start: 0.8528 (ttpp) cc_final: 0.7881 (pttm) REVERT: B 226 ASP cc_start: 0.9043 (t70) cc_final: 0.8496 (t0) REVERT: B 336 VAL cc_start: 0.9267 (m) cc_final: 0.9036 (t) REVERT: B 337 SER cc_start: 0.8895 (m) cc_final: 0.8363 (p) REVERT: B 418 GLN cc_start: 0.5776 (OUTLIER) cc_final: 0.5474 (mp10) REVERT: B 484 GLU cc_start: 0.7572 (pp20) cc_final: 0.6980 (mt-10) REVERT: B 486 ARG cc_start: 0.8271 (ttm170) cc_final: 0.7628 (ttm-80) REVERT: C 64 MET cc_start: 0.8734 (ttt) cc_final: 0.8297 (ttt) REVERT: C 141 ARG cc_start: 0.8058 (mtt90) cc_final: 0.7437 (mtt90) REVERT: C 208 VAL cc_start: 0.9041 (t) cc_final: 0.8718 (m) REVERT: D 105 GLU cc_start: 0.7983 (mp0) cc_final: 0.7293 (mp0) REVERT: D 393 MET cc_start: 0.7823 (tpt) cc_final: 0.7498 (tpp) REVERT: D 401 LYS cc_start: 0.7380 (mtpp) cc_final: 0.7015 (mtmm) REVERT: D 406 ARG cc_start: 0.7487 (mtt180) cc_final: 0.6956 (mtt90) REVERT: E 75 LYS cc_start: 0.7911 (ttpt) cc_final: 0.7631 (ttpp) REVERT: E 135 GLU cc_start: 0.8446 (mp0) cc_final: 0.8111 (mp0) REVERT: E 192 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7777 (ptm-80) REVERT: E 282 GLN cc_start: 0.8683 (pt0) cc_final: 0.8449 (pt0) REVERT: E 373 LYS cc_start: 0.8515 (mttm) cc_final: 0.8184 (mtpp) REVERT: F 126 GLU cc_start: 0.7785 (mt-10) cc_final: 0.6909 (mt-10) REVERT: F 261 PHE cc_start: 0.8382 (t80) cc_final: 0.8102 (t80) REVERT: F 300 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7907 (mttp) REVERT: F 325 THR cc_start: 0.9016 (m) cc_final: 0.8619 (p) REVERT: G 18 LYS cc_start: 0.7922 (ttmm) cc_final: 0.7558 (ttpp) REVERT: G 33 LYS cc_start: 0.8095 (mttm) cc_final: 0.7516 (tttm) REVERT: G 218 MET cc_start: 0.8023 (ttm) cc_final: 0.7561 (ttm) REVERT: G 242 LYS cc_start: 0.8611 (tppt) cc_final: 0.8106 (ttpt) REVERT: G 254 LEU cc_start: 0.8825 (tp) cc_final: 0.8599 (tp) outliers start: 84 outliers final: 74 residues processed: 693 average time/residue: 0.3476 time to fit residues: 377.6591 Evaluate side-chains 729 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 653 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 269 optimal weight: 3.9990 chunk 283 optimal weight: 5.9990 chunk 258 optimal weight: 0.9990 chunk 275 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 chunk 260 optimal weight: 0.9990 chunk 274 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 304 HIS ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23527 Z= 0.208 Angle : 0.553 11.917 31959 Z= 0.278 Chirality : 0.044 0.343 3809 Planarity : 0.004 0.044 4113 Dihedral : 6.845 164.532 3486 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.73 % Allowed : 21.37 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: 0.69 (0.15), residues: 3092 helix: 1.10 (0.15), residues: 1273 sheet: 0.35 (0.24), residues: 464 loop : 0.01 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 258 HIS 0.004 0.001 HIS A 145 PHE 0.020 0.001 PHE F 261 TYR 0.029 0.001 TYR C 473 ARG 0.009 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 657 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8617 (tp) cc_final: 0.8291 (tp) REVERT: A 228 MET cc_start: 0.8140 (tpt) cc_final: 0.7712 (tpt) REVERT: A 436 SER cc_start: 0.8516 (m) cc_final: 0.8104 (t) REVERT: A 465 GLU cc_start: 0.7638 (pt0) cc_final: 0.7372 (pt0) REVERT: B 91 LYS cc_start: 0.8498 (mmmm) cc_final: 0.8180 (mmmt) REVERT: B 189 LYS cc_start: 0.8506 (ttpp) cc_final: 0.7847 (pttm) REVERT: B 226 ASP cc_start: 0.9040 (t70) cc_final: 0.8508 (t0) REVERT: B 336 VAL cc_start: 0.9259 (m) cc_final: 0.9023 (t) REVERT: B 337 SER cc_start: 0.8907 (m) cc_final: 0.8364 (p) REVERT: B 418 GLN cc_start: 0.5778 (OUTLIER) cc_final: 0.5453 (mp10) REVERT: B 486 ARG cc_start: 0.8292 (ttm170) cc_final: 0.7627 (ttm-80) REVERT: C 64 MET cc_start: 0.8735 (ttt) cc_final: 0.8323 (ttt) REVERT: C 141 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7475 (mtt90) REVERT: C 208 VAL cc_start: 0.9043 (t) cc_final: 0.8737 (m) REVERT: C 486 ARG cc_start: 0.7163 (ttm-80) cc_final: 0.6958 (ttp80) REVERT: D 105 GLU cc_start: 0.7926 (mp0) cc_final: 0.7272 (mp0) REVERT: D 393 MET cc_start: 0.7851 (tpt) cc_final: 0.7415 (tpt) REVERT: D 401 LYS cc_start: 0.7393 (mtpp) cc_final: 0.7010 (mtmm) REVERT: D 406 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7010 (mtt90) REVERT: E 75 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7635 (ttpp) REVERT: E 135 GLU cc_start: 0.8454 (mp0) cc_final: 0.8004 (mp0) REVERT: E 136 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8773 (t) REVERT: E 192 ARG cc_start: 0.8230 (ttp80) cc_final: 0.7626 (ptt90) REVERT: E 282 GLN cc_start: 0.8681 (pt0) cc_final: 0.8453 (pt0) REVERT: E 373 LYS cc_start: 0.8508 (mttm) cc_final: 0.8175 (mtpp) REVERT: F 126 GLU cc_start: 0.7785 (mt-10) cc_final: 0.6891 (mt-10) REVERT: F 214 LYS cc_start: 0.8529 (pttm) cc_final: 0.8095 (pttp) REVERT: F 241 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7658 (tt0) REVERT: F 261 PHE cc_start: 0.8405 (t80) cc_final: 0.8112 (t80) REVERT: F 300 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7987 (mttp) REVERT: F 325 THR cc_start: 0.8987 (m) cc_final: 0.8570 (p) REVERT: G 18 LYS cc_start: 0.7810 (ttmm) cc_final: 0.7446 (ttpp) REVERT: G 33 LYS cc_start: 0.8090 (mttm) cc_final: 0.7508 (tttm) REVERT: G 218 MET cc_start: 0.7996 (ttm) cc_final: 0.7528 (ttm) REVERT: G 242 LYS cc_start: 0.8616 (tppt) cc_final: 0.8105 (ttpt) REVERT: G 254 LEU cc_start: 0.8821 (tp) cc_final: 0.8594 (tp) outliers start: 88 outliers final: 76 residues processed: 702 average time/residue: 0.3631 time to fit residues: 405.2617 Evaluate side-chains 732 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 653 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 181 optimal weight: 8.9990 chunk 291 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 305 optimal weight: 5.9990 chunk 281 optimal weight: 0.6980 chunk 243 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 HIS D 308 GLN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 23527 Z= 0.379 Angle : 0.634 12.380 31959 Z= 0.320 Chirality : 0.047 0.344 3809 Planarity : 0.004 0.051 4113 Dihedral : 7.194 164.923 3486 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.56 % Allowed : 21.50 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: 0.43 (0.15), residues: 3092 helix: 0.98 (0.15), residues: 1238 sheet: 0.07 (0.24), residues: 483 loop : -0.16 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 258 HIS 0.006 0.001 HIS A 478 PHE 0.020 0.002 PHE F 261 TYR 0.038 0.002 TYR B 399 ARG 0.010 0.001 ARG B 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 671 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLN cc_start: 0.8383 (tt0) cc_final: 0.8142 (tt0) REVERT: A 218 LEU cc_start: 0.8683 (tp) cc_final: 0.8279 (tp) REVERT: A 228 MET cc_start: 0.8229 (tpt) cc_final: 0.7739 (tpt) REVERT: A 436 SER cc_start: 0.8622 (m) cc_final: 0.8173 (t) REVERT: A 465 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7605 (pt0) REVERT: B 91 LYS cc_start: 0.8567 (mmmm) cc_final: 0.8212 (mmtp) REVERT: B 189 LYS cc_start: 0.8614 (ttpp) cc_final: 0.7961 (pttm) REVERT: B 205 TYR cc_start: 0.8593 (t80) cc_final: 0.8221 (t80) REVERT: B 226 ASP cc_start: 0.9075 (t70) cc_final: 0.8543 (t0) REVERT: B 335 ASP cc_start: 0.8352 (t0) cc_final: 0.8056 (t0) REVERT: B 336 VAL cc_start: 0.9296 (m) cc_final: 0.8922 (t) REVERT: B 337 SER cc_start: 0.9127 (m) cc_final: 0.8544 (p) REVERT: B 418 GLN cc_start: 0.5829 (OUTLIER) cc_final: 0.5538 (mp10) REVERT: B 486 ARG cc_start: 0.8320 (ttm170) cc_final: 0.7565 (ttm-80) REVERT: C 64 MET cc_start: 0.8677 (ttt) cc_final: 0.8091 (ttm) REVERT: C 141 ARG cc_start: 0.8062 (mtt90) cc_final: 0.7547 (mtt90) REVERT: C 208 VAL cc_start: 0.9063 (t) cc_final: 0.8777 (m) REVERT: C 276 GLN cc_start: 0.8707 (tt0) cc_final: 0.8373 (tt0) REVERT: D 35 ASN cc_start: 0.8598 (m-40) cc_final: 0.8187 (t0) REVERT: D 105 GLU cc_start: 0.7956 (mp0) cc_final: 0.7174 (mp0) REVERT: D 391 LEU cc_start: 0.7516 (tt) cc_final: 0.7246 (tt) REVERT: D 393 MET cc_start: 0.7884 (tpt) cc_final: 0.7526 (tpt) REVERT: D 401 LYS cc_start: 0.7486 (mtpp) cc_final: 0.7059 (mtmm) REVERT: D 406 ARG cc_start: 0.7462 (mtt180) cc_final: 0.7145 (mtt90) REVERT: E 75 LYS cc_start: 0.7919 (ttpt) cc_final: 0.7611 (ttpp) REVERT: E 136 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8801 (t) REVERT: E 192 ARG cc_start: 0.8374 (ttp80) cc_final: 0.7721 (ptt90) REVERT: E 282 GLN cc_start: 0.8757 (pt0) cc_final: 0.8488 (pt0) REVERT: E 373 LYS cc_start: 0.8509 (mttm) cc_final: 0.8172 (mtpp) REVERT: F 126 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7012 (mt-10) REVERT: F 130 SER cc_start: 0.7684 (OUTLIER) cc_final: 0.7401 (m) REVERT: F 241 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7648 (tt0) REVERT: F 325 THR cc_start: 0.8925 (m) cc_final: 0.8472 (p) REVERT: G 18 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7620 (ttpp) REVERT: G 33 LYS cc_start: 0.8117 (mttm) cc_final: 0.7500 (tttp) REVERT: G 180 LYS cc_start: 0.6066 (pttm) cc_final: 0.5804 (ptpt) REVERT: G 218 MET cc_start: 0.7943 (ttm) cc_final: 0.7417 (ttm) REVERT: G 242 LYS cc_start: 0.8615 (tppt) cc_final: 0.8118 (ttpt) REVERT: G 254 LEU cc_start: 0.8836 (tp) cc_final: 0.8562 (tp) REVERT: G 265 ASN cc_start: 0.8904 (m-40) cc_final: 0.8566 (m110) outliers start: 84 outliers final: 71 residues processed: 711 average time/residue: 0.3433 time to fit residues: 384.7097 Evaluate side-chains 732 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 657 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 193 optimal weight: 0.8980 chunk 259 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 243 optimal weight: 2.9990 chunk 102 optimal weight: 0.3980 chunk 250 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.129012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.109183 restraints weight = 32744.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.112576 restraints weight = 17051.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.114844 restraints weight = 10543.460| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23527 Z= 0.172 Angle : 0.557 12.025 31959 Z= 0.280 Chirality : 0.044 0.323 3809 Planarity : 0.004 0.044 4113 Dihedral : 6.863 167.223 3486 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.71 % Allowed : 22.73 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: 0.61 (0.15), residues: 3092 helix: 1.10 (0.15), residues: 1255 sheet: 0.21 (0.24), residues: 482 loop : -0.06 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 258 HIS 0.004 0.001 HIS D 178 PHE 0.018 0.001 PHE F 261 TYR 0.029 0.001 TYR C 473 ARG 0.010 0.000 ARG B 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6524.87 seconds wall clock time: 117 minutes 40.15 seconds (7060.15 seconds total)