Starting phenix.real_space_refine on Sat Feb 7 22:39:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hpo_52336/02_2026/9hpo_52336.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hpo_52336/02_2026/9hpo_52336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hpo_52336/02_2026/9hpo_52336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hpo_52336/02_2026/9hpo_52336.map" model { file = "/net/cci-nas-00/data/ceres_data/9hpo_52336/02_2026/9hpo_52336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hpo_52336/02_2026/9hpo_52336.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 168 5.16 5 C 23338 2.51 5 N 6444 2.21 5 O 7299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 155 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37273 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3159 Classifications: {'peptide': 410} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 394} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 3152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3152 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 14, 'TRANS': 394} Chain breaks: 2 Chain: "C" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3134 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 14, 'TRANS': 392} Chain breaks: 2 Chain: "D" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3019 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 378} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 378} Chain breaks: 4 Chain: "F" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2992 Classifications: {'peptide': 386} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 373} Chain breaks: 4 Chain: "G" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3159 Classifications: {'peptide': 410} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 394} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 3152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3152 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 14, 'TRANS': 394} Chain breaks: 2 Chain: "I" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3149 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 14, 'TRANS': 394} Chain breaks: 2 Chain: "J" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2950 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 369} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3030 Classifications: {'peptide': 391} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 378} Chain breaks: 4 Chain: "L" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3031 Classifications: {'peptide': 391} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 377} Chain breaks: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.01, per 1000 atoms: 0.24 Number of scatterers: 37273 At special positions: 0 Unit cell: (158.025, 172.86, 155.445, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 24 15.00 O 7299 8.00 N 6444 7.00 C 23338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.7 seconds 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8862 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 62 sheets defined 48.4% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 11 through 16 removed outlier: 3.846A pdb=" N ILE A 15 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 43 through 58 Processing helix chain 'A' and resid 75 through 87 Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 107 through 118 Processing helix chain 'A' and resid 173 through 183 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 241 through 249 removed outlier: 4.197A pdb=" N ALA A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.898A pdb=" N SER A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 409 through 421 Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 439 through 449 Processing helix chain 'B' and resid 11 through 16 Processing helix chain 'B' and resid 42 through 58 Processing helix chain 'B' and resid 75 through 88 Processing helix chain 'B' and resid 99 through 102 removed outlier: 3.719A pdb=" N TYR B 102 " --> pdb=" O SER B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 173 through 183 Processing helix chain 'B' and resid 206 through 210 removed outlier: 3.576A pdb=" N TYR B 209 " --> pdb=" O CYS B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 247 Processing helix chain 'B' and resid 274 through 289 Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.844A pdb=" N SER B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 350 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 387 through 401 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 409 through 421 removed outlier: 3.533A pdb=" N ALA B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'C' and resid 11 through 17 removed outlier: 3.558A pdb=" N ILE C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 58 Processing helix chain 'C' and resid 75 through 87 Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 107 through 118 Processing helix chain 'C' and resid 173 through 183 Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 240 through 247 Processing helix chain 'C' and resid 275 through 290 Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.892A pdb=" N SER C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 367 through 383 Processing helix chain 'C' and resid 387 through 401 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 409 through 420 Processing helix chain 'C' and resid 426 through 436 Processing helix chain 'C' and resid 439 through 451 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.865A pdb=" N ALA D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 114 through 126 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.863A pdb=" N LEU D 182 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 269 through 287 Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 317 Processing helix chain 'D' and resid 347 through 353 removed outlier: 4.164A pdb=" N ARG D 353 " --> pdb=" O ASP D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 378 Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 398 through 416 Processing helix chain 'D' and resid 422 through 431 removed outlier: 3.519A pdb=" N SER D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 447 Processing helix chain 'E' and resid 49 through 66 Processing helix chain 'E' and resid 82 through 95 removed outlier: 3.561A pdb=" N GLY E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 109 Processing helix chain 'E' and resid 114 through 126 Processing helix chain 'E' and resid 175 through 185 Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 269 through 287 Processing helix chain 'E' and resid 301 through 304 Processing helix chain 'E' and resid 305 through 316 Processing helix chain 'E' and resid 347 through 353 removed outlier: 4.328A pdb=" N ARG E 353 " --> pdb=" O ASP E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 379 Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 398 through 416 removed outlier: 3.517A pdb=" N ALA E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG E 416 " --> pdb=" O VAL E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 432 Processing helix chain 'E' and resid 435 through 448 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.538A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 114 through 126 removed outlier: 3.649A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 185 Processing helix chain 'F' and resid 244 through 252 Processing helix chain 'F' and resid 270 through 287 Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 316 Processing helix chain 'F' and resid 343 through 346 Processing helix chain 'F' and resid 347 through 353 removed outlier: 4.544A pdb=" N ARG F 353 " --> pdb=" O ASP F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 378 Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.511A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG F 416 " --> pdb=" O VAL F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 432 Processing helix chain 'F' and resid 435 through 447 removed outlier: 3.515A pdb=" N TYR F 446 " --> pdb=" O TYR F 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 19 removed outlier: 3.926A pdb=" N SER G 19 " --> pdb=" O ALA G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 58 Processing helix chain 'G' and resid 75 through 88 Processing helix chain 'G' and resid 99 through 102 Processing helix chain 'G' and resid 107 through 119 Processing helix chain 'G' and resid 173 through 183 Processing helix chain 'G' and resid 208 through 210 No H-bonds generated for 'chain 'G' and resid 208 through 210' Processing helix chain 'G' and resid 240 through 249 removed outlier: 4.429A pdb=" N ALA G 246 " --> pdb=" O ASP G 242 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN G 247 " --> pdb=" O LEU G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 290 Processing helix chain 'G' and resid 304 through 307 Processing helix chain 'G' and resid 308 through 321 removed outlier: 4.078A pdb=" N SER G 321 " --> pdb=" O ARG G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 347 through 350 Processing helix chain 'G' and resid 351 through 356 Processing helix chain 'G' and resid 367 through 382 Processing helix chain 'G' and resid 387 through 401 Processing helix chain 'G' and resid 402 through 420 removed outlier: 3.751A pdb=" N SER G 406 " --> pdb=" O THR G 402 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU G 410 " --> pdb=" O SER G 406 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR G 411 " --> pdb=" O VAL G 407 " (cutoff:3.500A) Proline residue: G 412 - end of helix Processing helix chain 'G' and resid 426 through 437 Processing helix chain 'G' and resid 439 through 449 Processing helix chain 'H' and resid 11 through 16 Processing helix chain 'H' and resid 42 through 58 Processing helix chain 'H' and resid 75 through 88 Processing helix chain 'H' and resid 99 through 102 Processing helix chain 'H' and resid 107 through 119 Processing helix chain 'H' and resid 173 through 183 Processing helix chain 'H' and resid 206 through 210 removed outlier: 3.652A pdb=" N TYR H 209 " --> pdb=" O CYS H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 247 Processing helix chain 'H' and resid 274 through 289 Processing helix chain 'H' and resid 303 through 307 Processing helix chain 'H' and resid 308 through 321 removed outlier: 3.701A pdb=" N SER H 321 " --> pdb=" O ARG H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 350 Processing helix chain 'H' and resid 351 through 356 Processing helix chain 'H' and resid 367 through 383 removed outlier: 3.823A pdb=" N LYS H 372 " --> pdb=" O PRO H 368 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN H 373 " --> pdb=" O GLN H 369 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE H 374 " --> pdb=" O GLU H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 401 Processing helix chain 'H' and resid 402 through 408 removed outlier: 3.608A pdb=" N SER H 406 " --> pdb=" O THR H 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 409 through 421 Processing helix chain 'H' and resid 426 through 435 removed outlier: 3.584A pdb=" N VAL H 430 " --> pdb=" O GLU H 426 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU H 431 " --> pdb=" O LYS H 427 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU H 432 " --> pdb=" O GLU H 428 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 451 removed outlier: 3.783A pdb=" N GLN H 450 " --> pdb=" O ILE H 446 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN H 451 " --> pdb=" O LEU H 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 17 removed outlier: 3.972A pdb=" N SER I 17 " --> pdb=" O GLN I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 59 removed outlier: 3.559A pdb=" N VAL I 51 " --> pdb=" O GLU I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 88 Processing helix chain 'I' and resid 99 through 101 No H-bonds generated for 'chain 'I' and resid 99 through 101' Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'I' and resid 173 through 183 Processing helix chain 'I' and resid 206 through 210 Processing helix chain 'I' and resid 240 through 247 Processing helix chain 'I' and resid 275 through 290 Processing helix chain 'I' and resid 303 through 307 Processing helix chain 'I' and resid 308 through 321 removed outlier: 3.889A pdb=" N SER I 321 " --> pdb=" O ARG I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 350 Processing helix chain 'I' and resid 351 through 356 Processing helix chain 'I' and resid 367 through 383 Processing helix chain 'I' and resid 387 through 401 Processing helix chain 'I' and resid 402 through 409 removed outlier: 3.595A pdb=" N SER I 406 " --> pdb=" O THR I 402 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 420 Processing helix chain 'I' and resid 426 through 437 Processing helix chain 'I' and resid 439 through 451 Processing helix chain 'J' and resid 49 through 66 Processing helix chain 'J' and resid 82 through 95 Processing helix chain 'J' and resid 106 through 108 No H-bonds generated for 'chain 'J' and resid 106 through 108' Processing helix chain 'J' and resid 114 through 126 Processing helix chain 'J' and resid 175 through 185 removed outlier: 3.657A pdb=" N THR J 183 " --> pdb=" O ILE J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 244 through 252 Processing helix chain 'J' and resid 269 through 287 removed outlier: 3.724A pdb=" N ARG J 273 " --> pdb=" O LYS J 269 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU J 286 " --> pdb=" O GLU J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 304 Processing helix chain 'J' and resid 305 through 317 Processing helix chain 'J' and resid 343 through 346 Processing helix chain 'J' and resid 347 through 353 removed outlier: 4.365A pdb=" N ARG J 353 " --> pdb=" O ASP J 349 " (cutoff:3.500A) Processing helix chain 'J' and resid 363 through 378 removed outlier: 3.500A pdb=" N THR J 367 " --> pdb=" O SER J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 397 Processing helix chain 'J' and resid 398 through 416 Processing helix chain 'J' and resid 422 through 431 removed outlier: 3.568A pdb=" N SER J 431 " --> pdb=" O LYS J 427 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 447 Processing helix chain 'K' and resid 49 through 66 Processing helix chain 'K' and resid 82 through 95 Processing helix chain 'K' and resid 106 through 109 Processing helix chain 'K' and resid 114 through 126 Processing helix chain 'K' and resid 175 through 185 Processing helix chain 'K' and resid 244 through 252 Processing helix chain 'K' and resid 269 through 287 Processing helix chain 'K' and resid 300 through 304 Processing helix chain 'K' and resid 305 through 316 Processing helix chain 'K' and resid 347 through 353 removed outlier: 4.256A pdb=" N ARG K 353 " --> pdb=" O ASP K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 379 Processing helix chain 'K' and resid 383 through 397 Processing helix chain 'K' and resid 398 through 416 removed outlier: 3.690A pdb=" N THR K 407 " --> pdb=" O ILE K 403 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA K 408 " --> pdb=" O GLN K 404 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG K 416 " --> pdb=" O VAL K 412 " (cutoff:3.500A) Processing helix chain 'K' and resid 422 through 432 Processing helix chain 'K' and resid 435 through 448 removed outlier: 3.613A pdb=" N GLN K 447 " --> pdb=" O MET K 443 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 66 removed outlier: 3.547A pdb=" N VAL L 58 " --> pdb=" O ARG L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 95 Processing helix chain 'L' and resid 106 through 109 removed outlier: 3.514A pdb=" N PHE L 109 " --> pdb=" O SER L 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 106 through 109' Processing helix chain 'L' and resid 114 through 126 Processing helix chain 'L' and resid 175 through 185 removed outlier: 3.564A pdb=" N LEU L 182 " --> pdb=" O MET L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 252 removed outlier: 3.659A pdb=" N ASN L 251 " --> pdb=" O ILE L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 286 Processing helix chain 'L' and resid 300 through 304 Processing helix chain 'L' and resid 305 through 317 removed outlier: 3.695A pdb=" N GLU L 317 " --> pdb=" O ASN L 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 343 through 346 Processing helix chain 'L' and resid 347 through 353 removed outlier: 4.456A pdb=" N ARG L 353 " --> pdb=" O ASP L 349 " (cutoff:3.500A) Processing helix chain 'L' and resid 363 through 378 Processing helix chain 'L' and resid 383 through 397 Processing helix chain 'L' and resid 398 through 416 removed outlier: 3.797A pdb=" N THR L 407 " --> pdb=" O ILE L 403 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA L 408 " --> pdb=" O GLN L 404 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG L 416 " --> pdb=" O VAL L 412 " (cutoff:3.500A) Processing helix chain 'L' and resid 422 through 433 Processing helix chain 'L' and resid 435 through 447 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.235A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.710A pdb=" N LYS A 201 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR A 192 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 189 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 158 through 159 Processing sheet with id=AA6, first strand: chain 'A' and resid 205 through 206 removed outlier: 5.367A pdb=" N ARG A 205 " --> pdb=" O VAL A 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA8, first strand: chain 'A' and resid 385 through 386 removed outlier: 7.598A pdb=" N ASN A 385 " --> pdb=" O ILE A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AB1, first strand: chain 'B' and resid 93 through 97 removed outlier: 6.212A pdb=" N CYS B 94 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASP B 302 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N MET B 96 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 66 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N SER B 331 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU B 68 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE B 360 " --> pdb=" O LEU E 434 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 434 " --> pdb=" O ILE B 360 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 229 through 239 removed outlier: 3.646A pdb=" N GLU B 126 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 170 through 171 removed outlier: 6.402A pdb=" N GLY B 160 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 336 through 337 Processing sheet with id=AB5, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.418A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 66 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N SER C 331 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU C 68 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU C 67 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE C 360 " --> pdb=" O LEU F 434 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 171 removed outlier: 3.501A pdb=" N ILE C 159 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE C 158 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU C 138 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY C 160 " --> pdb=" O THR C 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 199 through 201 removed outlier: 3.569A pdb=" N ALA C 199 " --> pdb=" O GLU C 194 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR C 192 " --> pdb=" O LYS C 201 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 437 through 438 removed outlier: 4.798A pdb=" N ILE E 356 " --> pdb=" O TYR C 438 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR E 359 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA E 76 " --> pdb=" O THR E 359 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR E 328 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU E 296 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA E 327 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE E 298 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.750A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 236 through 243 Processing sheet with id=AC2, first strand: chain 'D' and resid 141 through 144 removed outlier: 7.511A pdb=" N THR D 162 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AC4, first strand: chain 'E' and resid 233 through 243 Processing sheet with id=AC5, first strand: chain 'E' and resid 141 through 144 removed outlier: 7.583A pdb=" N THR E 162 " --> pdb=" O VAL E 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 192 through 193 Processing sheet with id=AC7, first strand: chain 'E' and resid 332 through 334 Processing sheet with id=AC8, first strand: chain 'E' and resid 381 through 382 removed outlier: 7.260A pdb=" N GLU E 381 " --> pdb=" O VAL E 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.122A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 240 through 243 Processing sheet with id=AD2, first strand: chain 'F' and resid 192 through 193 removed outlier: 3.666A pdb=" N ILE F 137 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS F 234 " --> pdb=" O ILE F 137 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 141 through 142 Processing sheet with id=AD4, first strand: chain 'F' and resid 333 through 334 Processing sheet with id=AD5, first strand: chain 'G' and resid 93 through 97 removed outlier: 6.442A pdb=" N CYS G 94 " --> pdb=" O PHE G 300 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASP G 302 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET G 96 " --> pdb=" O ASP G 302 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL G 66 " --> pdb=" O PHE G 329 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N SER G 331 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU G 68 " --> pdb=" O SER G 331 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 170 through 171 removed outlier: 5.817A pdb=" N ILE G 158 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU G 138 " --> pdb=" O ILE G 158 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY G 160 " --> pdb=" O THR G 136 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 238 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 199 through 201 removed outlier: 3.809A pdb=" N ASP G 189 " --> pdb=" O VAL G 135 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 205 through 206 removed outlier: 5.223A pdb=" N ARG G 205 " --> pdb=" O VAL G 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'G' and resid 336 through 337 Processing sheet with id=AE1, first strand: chain 'H' and resid 35 through 36 Processing sheet with id=AE2, first strand: chain 'H' and resid 93 through 97 removed outlier: 6.345A pdb=" N CYS H 94 " --> pdb=" O PHE H 300 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ASP H 302 " --> pdb=" O CYS H 94 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N MET H 96 " --> pdb=" O ASP H 302 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL H 66 " --> pdb=" O PHE H 329 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N SER H 331 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU H 68 " --> pdb=" O SER H 331 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE H 360 " --> pdb=" O LEU K 434 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 168 through 171 removed outlier: 6.454A pdb=" N GLY H 160 " --> pdb=" O THR H 136 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 199 through 201 removed outlier: 3.583A pdb=" N LYS H 201 " --> pdb=" O TYR H 192 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR H 192 " --> pdb=" O LYS H 201 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 336 through 337 Processing sheet with id=AE6, first strand: chain 'I' and resid 35 through 36 Processing sheet with id=AE7, first strand: chain 'I' and resid 93 through 97 removed outlier: 6.415A pdb=" N CYS I 94 " --> pdb=" O PHE I 300 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP I 302 " --> pdb=" O CYS I 94 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET I 96 " --> pdb=" O ASP I 302 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL I 66 " --> pdb=" O PHE I 329 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N SER I 331 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU I 68 " --> pdb=" O SER I 331 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU I 67 " --> pdb=" O ILE I 361 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 229 through 239 removed outlier: 3.604A pdb=" N VAL I 238 " --> pdb=" O LEU I 122 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 167 through 171 removed outlier: 6.755A pdb=" N ILE I 158 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU I 138 " --> pdb=" O ILE I 158 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY I 160 " --> pdb=" O THR I 136 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR I 192 " --> pdb=" O LYS I 201 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA I 199 " --> pdb=" O GLU I 194 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 385 through 386 removed outlier: 7.192A pdb=" N ASN I 385 " --> pdb=" O ILE I 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'J' and resid 100 through 104 removed outlier: 6.231A pdb=" N THR J 101 " --> pdb=" O PHE J 297 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASP J 299 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE J 103 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU J 296 " --> pdb=" O ILE J 325 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA J 327 " --> pdb=" O LEU J 296 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE J 298 " --> pdb=" O ALA J 327 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR J 328 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA J 72 " --> pdb=" O LEU J 355 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL J 357 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU J 74 " --> pdb=" O VAL J 357 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 238 through 243 Processing sheet with id=AF4, first strand: chain 'J' and resid 137 through 138 Processing sheet with id=AF5, first strand: chain 'J' and resid 141 through 144 removed outlier: 7.413A pdb=" N THR J 162 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 333 through 334 Processing sheet with id=AF7, first strand: chain 'K' and resid 100 through 104 removed outlier: 6.086A pdb=" N THR K 101 " --> pdb=" O PHE K 297 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASP K 299 " --> pdb=" O THR K 101 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE K 103 " --> pdb=" O ASP K 299 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU K 296 " --> pdb=" O ILE K 325 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ALA K 327 " --> pdb=" O LEU K 296 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE K 298 " --> pdb=" O ALA K 327 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA K 72 " --> pdb=" O LEU K 355 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL K 357 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU K 74 " --> pdb=" O VAL K 357 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 241 through 243 Processing sheet with id=AF9, first strand: chain 'K' and resid 133 through 135 Processing sheet with id=AG1, first strand: chain 'K' and resid 141 through 144 removed outlier: 7.296A pdb=" N THR K 162 " --> pdb=" O VAL K 143 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 192 through 193 Processing sheet with id=AG3, first strand: chain 'K' and resid 332 through 334 Processing sheet with id=AG4, first strand: chain 'K' and resid 381 through 382 removed outlier: 7.176A pdb=" N GLU K 381 " --> pdb=" O VAL K 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'L' and resid 100 through 104 removed outlier: 6.187A pdb=" N THR L 101 " --> pdb=" O PHE L 297 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP L 299 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE L 103 " --> pdb=" O ASP L 299 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU L 296 " --> pdb=" O ILE L 325 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ALA L 327 " --> pdb=" O LEU L 296 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE L 298 " --> pdb=" O ALA L 327 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU L 74 " --> pdb=" O VAL L 357 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR L 359 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA L 76 " --> pdb=" O THR L 359 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 233 through 243 Processing sheet with id=AG7, first strand: chain 'L' and resid 141 through 144 removed outlier: 3.583A pdb=" N VAL L 143 " --> pdb=" O THR L 162 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR L 162 " --> pdb=" O VAL L 143 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 333 through 334 1808 hydrogen bonds defined for protein. 5175 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: 7.97 Time building geometry restraints manager: 3.96 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: 8643 1.33 - 1.45: 6617 1.45 - 1.57: 22134 1.57 - 1.69: 36 1.69 - 1.82: 282 Bond restraints: 37712 Sorted by residual: bond pdb=" C4 ADP D 501 " pdb=" C5 ADP D 501 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP J 501 " pdb=" C5 ADP J 501 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C5 ADP F 501 " pdb=" C6 ADP F 501 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C5 ADP J 501 " pdb=" C6 ADP J 501 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 37707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 50262 2.62 - 5.25: 513 5.25 - 7.87: 66 7.87 - 10.50: 15 10.50 - 13.12: 7 Bond angle restraints: 50863 Sorted by residual: angle pdb=" CA ASP F 34 " pdb=" CB ASP F 34 " pdb=" CG ASP F 34 " ideal model delta sigma weight residual 112.60 119.17 -6.57 1.00e+00 1.00e+00 4.32e+01 angle pdb=" N LYS G 7 " pdb=" CA LYS G 7 " pdb=" C LYS G 7 " ideal model delta sigma weight residual 110.42 101.50 8.92 1.46e+00 4.69e-01 3.74e+01 angle pdb=" C LYS G 7 " pdb=" CA LYS G 7 " pdb=" CB LYS G 7 " ideal model delta sigma weight residual 109.71 117.78 -8.07 1.39e+00 5.18e-01 3.37e+01 angle pdb=" N SER G 8 " pdb=" CA SER G 8 " pdb=" C SER G 8 " ideal model delta sigma weight residual 110.50 104.33 6.17 1.41e+00 5.03e-01 1.92e+01 angle pdb=" C5' ADP I 501 " pdb=" C4' ADP I 501 " pdb=" O4' ADP I 501 " ideal model delta sigma weight residual 109.47 122.59 -13.12 3.00e+00 1.11e-01 1.91e+01 ... (remaining 50858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 22188 35.09 - 70.19: 1013 70.19 - 105.28: 89 105.28 - 140.38: 3 140.38 - 175.47: 6 Dihedral angle restraints: 23299 sinusoidal: 9591 harmonic: 13708 Sorted by residual: dihedral pdb=" O2A ADP J 501 " pdb=" O3A ADP J 501 " pdb=" PA ADP J 501 " pdb=" PB ADP J 501 " ideal model delta sinusoidal sigma weight residual -60.00 115.47 -175.47 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP L 501 " pdb=" O5' ADP L 501 " pdb=" PA ADP L 501 " pdb=" O2A ADP L 501 " ideal model delta sinusoidal sigma weight residual 300.00 134.69 165.31 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 139.29 160.72 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 23296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.351: 6038 0.351 - 0.701: 0 0.701 - 1.052: 0 1.052 - 1.402: 0 1.402 - 1.752: 2 Chirality restraints: 6040 Sorted by residual: chirality pdb=" C4' ADP I 501 " pdb=" C3' ADP I 501 " pdb=" C5' ADP I 501 " pdb=" O4' ADP I 501 " both_signs ideal model delta sigma weight residual False -2.50 -0.75 -1.75 2.00e-01 2.50e+01 7.68e+01 chirality pdb=" C4' ADP C 501 " pdb=" C3' ADP C 501 " pdb=" C5' ADP C 501 " pdb=" O4' ADP C 501 " both_signs ideal model delta sigma weight residual False -2.50 -0.79 -1.71 2.00e-01 2.50e+01 7.31e+01 chirality pdb=" CG LEU A 415 " pdb=" CB LEU A 415 " pdb=" CD1 LEU A 415 " pdb=" CD2 LEU A 415 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.23e-01 ... (remaining 6037 not shown) Planarity restraints: 6444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 283 " -0.018 2.00e-02 2.50e+03 1.76e-02 7.77e+00 pdb=" CG TRP E 283 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP E 283 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP E 283 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 283 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 283 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 283 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 283 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 283 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 283 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 335 " -0.014 2.00e-02 2.50e+03 2.72e-02 7.39e+00 pdb=" CG ASN A 335 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 335 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 335 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 283 " 0.021 2.00e-02 2.50e+03 1.60e-02 6.42e+00 pdb=" CG TRP D 283 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP D 283 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP D 283 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 283 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 283 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 283 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 283 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 283 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 283 " 0.004 2.00e-02 2.50e+03 ... (remaining 6441 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 186 2.52 - 3.12: 31607 3.12 - 3.71: 59938 3.71 - 4.31: 84777 4.31 - 4.90: 134458 Nonbonded interactions: 310966 Sorted by model distance: nonbonded pdb=" NE2 GLN L 78 " pdb=" CD PRO L 79 " model vdw 1.931 3.520 nonbonded pdb=" OE2 GLU B 100 " pdb=" NH1 ARG D 314 " model vdw 2.252 3.120 nonbonded pdb=" CG LYS L 160 " pdb=" CG2 ILE L 171 " model vdw 2.269 3.860 nonbonded pdb=" CE2 TYR D 446 " pdb=" OE1 GLN D 447 " model vdw 2.295 3.340 nonbonded pdb=" OG SER A 17 " pdb=" O3' ADP A 501 " model vdw 2.297 3.040 ... (remaining 310961 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 247 or resid 274 through 501)) selection = (chain 'B' and (resid 6 through 247 or resid 274 through 448 or (resid 449 and ( \ name N or name CA or name C or name CB or name CG or name OD1 or name OD2)) or r \ esid 450 through 501)) selection = (chain 'C' and (resid 6 through 247 or resid 274 through 448 or (resid 449 and ( \ name N or name CA or name C or name CB or name CG or name OD1 or name OD2)) or r \ esid 450 through 501)) selection = (chain 'G' and (resid 6 through 247 or resid 274 through 501)) selection = (chain 'H' and (resid 6 through 247 or resid 274 through 448 or (resid 449 and ( \ name N or name CA or name C or name CB or name CG or name OD1 or name OD2)) or r \ esid 450 through 501)) selection = (chain 'I' and (resid 6 through 247 or resid 274 through 448 or (resid 449 and ( \ name N or name CA or name C or name CB or name CG or name OD1 or name OD2)) or r \ esid 450 through 501)) } ncs_group { reference = (chain 'D' and (resid 23 through 147 or resid 158 through 252 or resid 267 throu \ gh 501)) selection = (chain 'E' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 252 or resid 267 through 447 or re \ sid 501)) selection = (chain 'F' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 252 or resid 267 through 501)) selection = (chain 'J' and (resid 23 through 147 or resid 158 through 252 or resid 267 throu \ gh 501)) selection = (chain 'K' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 147 or resid 158 through 252 or re \ sid 267 through 447 or resid 501)) selection = (chain 'L' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 147 or resid 158 through 252 or re \ sid 267 through 501)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 34.750 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.090 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 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 0.110 37712 Z= 0.169 Angle : 0.693 13.120 50863 Z= 0.375 Chirality : 0.050 1.752 6040 Planarity : 0.004 0.046 6444 Dihedral : 19.388 175.471 14437 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 47.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.04 % Rotamer: Outliers : 2.30 % Allowed : 36.39 % Favored : 61.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.12), residues: 4693 helix: 1.07 (0.11), residues: 2149 sheet: -1.58 (0.20), residues: 688 loop : -2.02 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 362 TYR 0.022 0.001 TYR A 192 PHE 0.021 0.001 PHE B 93 TRP 0.048 0.004 TRP E 283 HIS 0.005 0.001 HIS G 429 Details of bonding type rmsd covalent geometry : bond 0.00326 (37712) covalent geometry : angle 0.69314 (50863) hydrogen bonds : bond 0.19924 ( 1808) hydrogen bonds : angle 8.09711 ( 5175) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 612 time to evaluate : 1.449 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 449 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7913 (tpt) cc_final: 0.7322 (tpt) REVERT: A 273 ASP cc_start: 0.6537 (t0) cc_final: 0.6328 (t70) REVERT: A 352 LEU cc_start: 0.6629 (mm) cc_final: 0.6151 (tp) REVERT: A 359 MET cc_start: 0.7440 (mtp) cc_final: 0.6950 (mtp) REVERT: A 400 LYS cc_start: 0.7425 (mtpp) cc_final: 0.7195 (tttp) REVERT: A 402 THR cc_start: 0.8737 (t) cc_final: 0.8502 (t) REVERT: A 442 SER cc_start: 0.7406 (m) cc_final: 0.7192 (m) REVERT: B 43 GLU cc_start: 0.6265 (mp0) cc_final: 0.5552 (mm-30) REVERT: B 345 THR cc_start: 0.7876 (t) cc_final: 0.7623 (t) REVERT: B 361 ILE cc_start: 0.7763 (mm) cc_final: 0.7535 (mt) REVERT: B 432 GLU cc_start: 0.5682 (pt0) cc_final: 0.4498 (mt-10) REVERT: B 446 ILE cc_start: 0.6227 (tt) cc_final: 0.5872 (mt) REVERT: C 54 GLU cc_start: 0.6637 (mm-30) cc_final: 0.6410 (mm-30) REVERT: C 90 LYS cc_start: 0.5671 (OUTLIER) cc_final: 0.5272 (mmtt) REVERT: C 123 ARG cc_start: 0.6379 (ttm-80) cc_final: 0.6027 (mtt90) REVERT: C 303 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6891 (mt-10) REVERT: C 317 ARG cc_start: 0.6123 (mmt90) cc_final: 0.5922 (mmm160) REVERT: C 335 ASN cc_start: 0.6883 (p0) cc_final: 0.6505 (t0) REVERT: C 364 MET cc_start: 0.7020 (mmm) cc_final: 0.6052 (mpp) REVERT: C 369 GLN cc_start: 0.5678 (mp10) cc_final: 0.5472 (pm20) REVERT: C 433 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6346 (tp) REVERT: D 46 MET cc_start: 0.7272 (mmt) cc_final: 0.6698 (mmt) REVERT: D 50 LEU cc_start: 0.7809 (pt) cc_final: 0.7357 (mt) REVERT: D 62 MET cc_start: 0.6829 (ttm) cc_final: 0.6585 (mtp) REVERT: D 78 GLN cc_start: 0.7107 (mp10) cc_final: 0.6679 (mt0) REVERT: D 124 ARG cc_start: 0.7114 (mmm-85) cc_final: 0.6811 (mmm160) REVERT: D 125 ARG cc_start: 0.6127 (mtm180) cc_final: 0.5882 (mtm-85) REVERT: D 303 MET cc_start: 0.7262 (tpp) cc_final: 0.6951 (tpp) REVERT: D 330 ARG cc_start: 0.6547 (mtp85) cc_final: 0.5844 (mtp180) REVERT: D 352 ASP cc_start: 0.6691 (m-30) cc_final: 0.5909 (m-30) REVERT: D 392 ARG cc_start: 0.6800 (mmm160) cc_final: 0.6445 (tmm160) REVERT: D 425 ASP cc_start: 0.6805 (m-30) cc_final: 0.6007 (t0) REVERT: D 444 LYS cc_start: 0.6143 (pttm) cc_final: 0.5883 (pttm) REVERT: D 445 GLU cc_start: 0.4019 (tm-30) cc_final: 0.3526 (mm-30) REVERT: E 65 GLU cc_start: 0.6300 (mt-10) cc_final: 0.5905 (mt-10) REVERT: E 88 MET cc_start: 0.7204 (tpp) cc_final: 0.6951 (mmm) REVERT: E 124 ARG cc_start: 0.6982 (mmt90) cc_final: 0.6299 (mtp180) REVERT: E 168 MET cc_start: 0.0792 (tmm) cc_final: 0.0335 (ptm) REVERT: E 279 LYS cc_start: 0.4077 (mtpt) cc_final: 0.3515 (mmtt) REVERT: E 283 TRP cc_start: 0.6221 (m-90) cc_final: 0.6014 (m-90) REVERT: E 314 ARG cc_start: 0.6180 (ttm-80) cc_final: 0.5964 (ttm-80) REVERT: E 356 ILE cc_start: 0.8125 (tt) cc_final: 0.7728 (mt) REVERT: E 365 LYS cc_start: 0.6097 (mtmm) cc_final: 0.5871 (ttpt) REVERT: E 391 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7272 (p) REVERT: F 67 LYS cc_start: 0.6368 (mtmt) cc_final: 0.6164 (mmtm) REVERT: F 88 MET cc_start: 0.7594 (tpp) cc_final: 0.7070 (tpt) REVERT: F 107 GLU cc_start: 0.7671 (mm-30) cc_final: 0.6772 (tt0) REVERT: F 126 SER cc_start: 0.8421 (m) cc_final: 0.8200 (p) REVERT: F 168 MET cc_start: -0.2537 (ptt) cc_final: -0.3102 (mtt) REVERT: F 269 LYS cc_start: 0.5001 (mtmm) cc_final: 0.4767 (mttp) REVERT: F 300 GLU cc_start: 0.6461 (mt-10) cc_final: 0.5668 (mm-30) REVERT: F 320 MET cc_start: 0.4367 (mtt) cc_final: 0.4022 (mmp) REVERT: F 330 ARG cc_start: 0.7290 (mmm-85) cc_final: 0.6878 (mmt90) REVERT: F 353 ARG cc_start: 0.7033 (ptt180) cc_final: 0.6244 (ptt180) REVERT: F 382 MET cc_start: 0.7084 (mmt) cc_final: 0.6878 (mmt) REVERT: G 18 HIS cc_start: 0.5735 (OUTLIER) cc_final: 0.4566 (p-80) REVERT: G 44 ASN cc_start: 0.5116 (m-40) cc_final: 0.4764 (t0) REVERT: G 114 GLU cc_start: 0.6224 (tt0) cc_final: 0.5789 (tp30) REVERT: G 310 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6255 (mp0) REVERT: G 364 MET cc_start: 0.6586 (ttm) cc_final: 0.6239 (ttm) REVERT: G 370 GLU cc_start: 0.6158 (mp0) cc_final: 0.5652 (mt-10) REVERT: G 400 LYS cc_start: 0.6446 (mmmm) cc_final: 0.5599 (mmtp) REVERT: G 426 GLU cc_start: 0.5142 (mt-10) cc_final: 0.4765 (tt0) REVERT: G 427 LYS cc_start: 0.4739 (tttm) cc_final: 0.4483 (tmmt) REVERT: G 439 ASP cc_start: 0.7208 (p0) cc_final: 0.6981 (p0) REVERT: H 14 ARG cc_start: 0.5474 (mmt90) cc_final: 0.5049 (mmt180) REVERT: H 39 LEU cc_start: 0.5876 (mt) cc_final: 0.5318 (mt) REVERT: H 43 GLU cc_start: 0.7007 (pm20) cc_final: 0.6336 (mm-30) REVERT: H 391 LEU cc_start: 0.5316 (OUTLIER) cc_final: 0.5021 (mt) REVERT: H 436 LEU cc_start: 0.6542 (mt) cc_final: 0.6187 (mt) REVERT: I 233 GLU cc_start: 0.2608 (OUTLIER) cc_final: 0.2278 (tt0) REVERT: I 306 MET cc_start: 0.7423 (ttp) cc_final: 0.7174 (ttm) REVERT: I 343 ASP cc_start: 0.6481 (m-30) cc_final: 0.6173 (t0) REVERT: I 360 ILE cc_start: 0.7948 (tt) cc_final: 0.7283 (mt) REVERT: I 363 THR cc_start: 0.7566 (m) cc_final: 0.6754 (p) REVERT: I 364 MET cc_start: 0.7866 (mmm) cc_final: 0.7441 (mmm) REVERT: I 388 GLU cc_start: 0.4265 (mm-30) cc_final: 0.2939 (tm-30) REVERT: J 109 PHE cc_start: 0.7132 (m-80) cc_final: 0.6836 (m-10) REVERT: J 134 GLU cc_start: 0.4112 (OUTLIER) cc_final: 0.3496 (tt0) REVERT: J 168 MET cc_start: 0.1603 (mtt) cc_final: 0.1078 (ptt) REVERT: J 178 MET cc_start: 0.0153 (mmp) cc_final: -0.0577 (mtt) REVERT: J 314 ARG cc_start: 0.7126 (tpp-160) cc_final: 0.6142 (mmm160) REVERT: J 320 MET cc_start: 0.5746 (mtm) cc_final: 0.5388 (mtt) REVERT: J 330 ARG cc_start: 0.4999 (mtt-85) cc_final: 0.4569 (mmt-90) REVERT: J 355 LEU cc_start: 0.7151 (mt) cc_final: 0.6920 (mt) REVERT: J 360 THR cc_start: 0.7634 (t) cc_final: 0.6523 (m) REVERT: J 380 VAL cc_start: 0.4994 (t) cc_final: 0.4683 (m) REVERT: J 382 MET cc_start: 0.5321 (tpp) cc_final: 0.3790 (ttm) REVERT: J 404 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6154 (tt0) REVERT: K 46 MET cc_start: 0.5138 (mtp) cc_final: 0.4614 (mtp) REVERT: K 168 MET cc_start: -0.0282 (ttm) cc_final: -0.1310 (mtp) REVERT: K 288 LYS cc_start: 0.2429 (mmtm) cc_final: 0.1913 (tttm) REVERT: K 303 MET cc_start: 0.7424 (mmt) cc_final: 0.7001 (mmm) REVERT: K 325 ILE cc_start: 0.7991 (mt) cc_final: 0.7786 (mt) REVERT: K 332 ILE cc_start: 0.7264 (pt) cc_final: 0.6950 (pt) REVERT: K 368 LYS cc_start: 0.5721 (tttt) cc_final: 0.5297 (ttpp) REVERT: L 31 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6403 (mp) REVERT: L 41 GLN cc_start: 0.5238 (tm-30) cc_final: 0.5024 (tp40) REVERT: L 62 MET cc_start: 0.5263 (mtt) cc_final: 0.5033 (mtt) REVERT: L 307 GLU cc_start: 0.6618 (tp30) cc_final: 0.5643 (mt-10) REVERT: L 358 SER cc_start: 0.7610 (p) cc_final: 0.7155 (t) REVERT: L 369 GLN cc_start: 0.6361 (mm-40) cc_final: 0.5376 (tt0) REVERT: L 436 GLU cc_start: 0.5453 (pp20) cc_final: 0.4877 (pm20) outliers start: 93 outliers final: 43 residues processed: 684 average time/residue: 0.2317 time to fit residues: 252.7543 Evaluate side-chains 495 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 443 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 442 TYR Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 391 LEU Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 238 VAL Chi-restraints excluded: chain I residue 344 ILE Chi-restraints excluded: chain I residue 367 THR Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 283 TRP Chi-restraints excluded: chain J residue 404 GLN Chi-restraints excluded: chain J residue 426 ILE Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 50 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 470 optimal weight: 2.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN C 13 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 GLN ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 392 ASN H 85 GLN H 115 ASN H 280 ASN H 335 ASN H 385 ASN H 408 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 GLN K 245 HIS ** L 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.225244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.208817 restraints weight = 42779.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.198322 restraints weight = 97507.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.194202 restraints weight = 87364.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.193282 restraints weight = 86381.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.193280 restraints weight = 53834.301| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4074 r_free = 0.4074 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4073 r_free = 0.4073 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 37712 Z= 0.209 Angle : 0.790 13.357 50863 Z= 0.393 Chirality : 0.049 0.254 6040 Planarity : 0.005 0.062 6444 Dihedral : 10.343 178.152 5343 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.52 % Favored : 94.35 % Rotamer: Outliers : 8.20 % Allowed : 27.69 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.12), residues: 4693 helix: 0.96 (0.11), residues: 2155 sheet: -1.62 (0.19), residues: 662 loop : -2.03 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 130 TYR 0.025 0.002 TYR B 192 PHE 0.017 0.002 PHE D 257 TRP 0.038 0.005 TRP J 283 HIS 0.009 0.002 HIS H 393 Details of bonding type rmsd covalent geometry : bond 0.00487 (37712) covalent geometry : angle 0.79043 (50863) hydrogen bonds : bond 0.04737 ( 1808) hydrogen bonds : angle 5.72408 ( 5175) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 332 poor density : 477 time to evaluate : 1.497 Fit side-chains TARDY: cannot create tardy model for: "ASP A 449 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 ASP cc_start: 0.6250 (OUTLIER) cc_final: 0.5961 (p0) REVERT: A 371 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7176 (mtp) REVERT: A 376 LYS cc_start: 0.7390 (tptp) cc_final: 0.6882 (mtmm) REVERT: B 306 MET cc_start: 0.8155 (tpp) cc_final: 0.7896 (mmt) REVERT: B 432 GLU cc_start: 0.5641 (pt0) cc_final: 0.4983 (mt-10) REVERT: C 54 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6605 (mm-30) REVERT: C 115 ASN cc_start: 0.8874 (m-40) cc_final: 0.8285 (m-40) REVERT: C 320 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6751 (tt0) REVERT: C 423 ASP cc_start: 0.5377 (p0) cc_final: 0.4853 (p0) REVERT: D 78 GLN cc_start: 0.7391 (mp10) cc_final: 0.7150 (mt0) REVERT: D 130 ARG cc_start: 0.6311 (ptp-110) cc_final: 0.5534 (ptp-170) REVERT: D 138 ILE cc_start: 0.1971 (OUTLIER) cc_final: 0.1546 (tp) REVERT: D 303 MET cc_start: 0.7896 (tpp) cc_final: 0.7659 (mmt) REVERT: E 37 LEU cc_start: 0.5008 (OUTLIER) cc_final: 0.4759 (mp) REVERT: E 124 ARG cc_start: 0.8207 (mmt90) cc_final: 0.7926 (mtp180) REVERT: E 179 ILE cc_start: 0.1396 (OUTLIER) cc_final: 0.1120 (pt) REVERT: E 279 LYS cc_start: 0.5999 (mtpt) cc_final: 0.5768 (mmtt) REVERT: E 349 ASP cc_start: 0.7528 (p0) cc_final: 0.7301 (p0) REVERT: E 356 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8362 (mt) REVERT: E 391 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8363 (p) REVERT: F 107 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7545 (tt0) REVERT: F 168 MET cc_start: -0.0601 (ptt) cc_final: -0.1356 (mtt) REVERT: F 173 ASP cc_start: 0.2406 (OUTLIER) cc_final: 0.1927 (t70) REVERT: F 353 ARG cc_start: 0.7620 (ptt180) cc_final: 0.6966 (ptt180) REVERT: F 360 THR cc_start: 0.8647 (t) cc_final: 0.8433 (p) REVERT: G 7 LYS cc_start: 0.5962 (OUTLIER) cc_final: 0.5704 (ptpt) REVERT: G 44 ASN cc_start: 0.5247 (m-40) cc_final: 0.4656 (t0) REVERT: G 64 ARG cc_start: 0.6723 (mtm-85) cc_final: 0.6505 (ttp-170) REVERT: G 310 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6464 (mp0) REVERT: G 345 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7869 (m) REVERT: G 399 THR cc_start: 0.6755 (OUTLIER) cc_final: 0.6524 (m) REVERT: G 400 LYS cc_start: 0.5823 (mmmm) cc_final: 0.5289 (mmtp) REVERT: G 435 GLU cc_start: 0.7458 (tp30) cc_final: 0.6962 (tp30) REVERT: H 26 LEU cc_start: 0.5354 (OUTLIER) cc_final: 0.5031 (mt) REVERT: H 39 LEU cc_start: 0.5701 (OUTLIER) cc_final: 0.5295 (mt) REVERT: H 77 THR cc_start: 0.7441 (p) cc_final: 0.7174 (m) REVERT: H 118 ARG cc_start: 0.6698 (mtt-85) cc_final: 0.6463 (mtp85) REVERT: H 352 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7186 (mm) REVERT: H 391 LEU cc_start: 0.5770 (OUTLIER) cc_final: 0.5473 (mt) REVERT: I 295 VAL cc_start: 0.6289 (p) cc_final: 0.6088 (p) REVERT: I 350 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8147 (mm) REVERT: I 360 ILE cc_start: 0.8116 (tt) cc_final: 0.7719 (mt) REVERT: I 363 THR cc_start: 0.8683 (m) cc_final: 0.8213 (p) REVERT: I 388 GLU cc_start: 0.3843 (mm-30) cc_final: 0.2465 (tm-30) REVERT: I 441 LYS cc_start: 0.7088 (tppt) cc_final: 0.6349 (mttp) REVERT: J 40 ARG cc_start: 0.4455 (mtm-85) cc_final: 0.3889 (mtp180) REVERT: J 134 GLU cc_start: 0.3839 (OUTLIER) cc_final: 0.3170 (tt0) REVERT: J 179 ILE cc_start: 0.1482 (OUTLIER) cc_final: 0.0929 (tp) REVERT: J 244 LEU cc_start: 0.7116 (mt) cc_final: 0.6652 (mt) REVERT: J 285 GLU cc_start: 0.1902 (OUTLIER) cc_final: 0.1530 (pt0) REVERT: J 291 ILE cc_start: 0.5779 (mp) cc_final: 0.5194 (tt) REVERT: J 314 ARG cc_start: 0.7100 (tpp-160) cc_final: 0.6674 (tpt170) REVERT: J 366 ASP cc_start: 0.5215 (OUTLIER) cc_final: 0.4844 (m-30) REVERT: J 422 GLN cc_start: 0.6097 (mm-40) cc_final: 0.5870 (mp10) REVERT: J 437 SER cc_start: 0.7722 (t) cc_final: 0.7367 (t) REVERT: J 441 GLN cc_start: 0.6952 (tm-30) cc_final: 0.6174 (pt0) REVERT: K 46 MET cc_start: 0.4423 (mtp) cc_final: 0.4112 (mtp) REVERT: K 50 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5753 (mt) REVERT: K 168 MET cc_start: 0.0890 (OUTLIER) cc_final: -0.1400 (mtp) REVERT: K 288 LYS cc_start: 0.2341 (mmtm) cc_final: 0.2098 (tttm) REVERT: K 388 THR cc_start: 0.6598 (p) cc_final: 0.5944 (t) REVERT: L 41 GLN cc_start: 0.5700 (tm-30) cc_final: 0.5166 (tp40) REVERT: L 71 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.7076 (mtm-85) REVERT: L 147 ILE cc_start: 0.0630 (OUTLIER) cc_final: 0.0313 (mt) REVERT: L 358 SER cc_start: 0.7436 (p) cc_final: 0.7045 (t) REVERT: L 369 GLN cc_start: 0.5189 (mm-40) cc_final: 0.4514 (mt0) REVERT: L 382 MET cc_start: 0.6153 (mtm) cc_final: 0.5198 (ttm) REVERT: L 385 ASP cc_start: 0.5350 (OUTLIER) cc_final: 0.4586 (t0) REVERT: L 437 SER cc_start: 0.7576 (m) cc_final: 0.7145 (m) REVERT: L 440 THR cc_start: 0.7582 (OUTLIER) cc_final: 0.7296 (p) outliers start: 332 outliers final: 174 residues processed: 760 average time/residue: 0.2293 time to fit residues: 284.0359 Evaluate side-chains 594 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 393 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 442 TYR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 113 MET Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 446 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain H residue 335 ASN Chi-restraints excluded: chain H residue 352 LEU Chi-restraints excluded: chain H residue 385 ASN Chi-restraints excluded: chain H residue 391 LEU Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 242 ASP Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 337 VAL Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 350 ILE Chi-restraints excluded: chain I residue 356 ASP Chi-restraints excluded: chain I residue 367 THR Chi-restraints excluded: chain I residue 433 ILE Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 283 TRP Chi-restraints excluded: chain J residue 285 GLU Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 352 ASP Chi-restraints excluded: chain J residue 358 SER Chi-restraints excluded: chain J residue 362 TYR Chi-restraints excluded: chain J residue 366 ASP Chi-restraints excluded: chain J residue 379 ASP Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 426 ILE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 168 MET Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 328 THR Chi-restraints excluded: chain K residue 338 THR Chi-restraints excluded: chain K residue 357 VAL Chi-restraints excluded: chain K residue 419 THR Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 257 PHE Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 364 GLU Chi-restraints excluded: chain L residue 379 ASP Chi-restraints excluded: chain L residue 385 ASP Chi-restraints excluded: chain L residue 440 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 62 optimal weight: 0.9980 chunk 147 optimal weight: 0.0670 chunk 67 optimal weight: 0.9990 chunk 344 optimal weight: 10.0000 chunk 356 optimal weight: 5.9990 chunk 462 optimal weight: 2.9990 chunk 396 optimal weight: 20.0000 chunk 197 optimal weight: 1.9990 chunk 467 optimal weight: 2.9990 chunk 339 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN C 156 HIS ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN E 369 GLN F 188 GLN G 241 HIS G 392 ASN H 42 GLN H 335 ASN H 373 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 HIS I 348 HIS I 420 ASN J 369 GLN L 27 HIS L 404 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.227522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.211059 restraints weight = 42737.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.200929 restraints weight = 95133.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.196277 restraints weight = 88786.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.195659 restraints weight = 86813.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.195602 restraints weight = 53542.677| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4062 r_free = 0.4062 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4061 r_free = 0.4061 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37712 Z= 0.136 Angle : 0.649 11.852 50863 Z= 0.321 Chirality : 0.045 0.225 6040 Planarity : 0.004 0.074 6444 Dihedral : 9.607 173.093 5299 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.73 % Favored : 95.16 % Rotamer: Outliers : 6.47 % Allowed : 27.94 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.12), residues: 4693 helix: 1.02 (0.11), residues: 2171 sheet: -1.54 (0.19), residues: 664 loop : -1.89 (0.13), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 276 TYR 0.020 0.001 TYR A 192 PHE 0.012 0.001 PHE L 257 TRP 0.029 0.003 TRP J 283 HIS 0.006 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00300 (37712) covalent geometry : angle 0.64940 (50863) hydrogen bonds : bond 0.03963 ( 1808) hydrogen bonds : angle 5.12236 ( 5175) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 414 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.6894 (tp30) cc_final: 0.6690 (tp30) REVERT: A 326 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7632 (tp) REVERT: A 364 MET cc_start: 0.6826 (mmt) cc_final: 0.6592 (mmp) REVERT: A 371 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.7079 (tpp) REVERT: A 376 LYS cc_start: 0.7457 (tptp) cc_final: 0.6889 (mtmm) REVERT: A 384 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7743 (mt) REVERT: B 279 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7538 (mm) REVERT: B 285 LYS cc_start: 0.6245 (OUTLIER) cc_final: 0.5982 (ttpp) REVERT: B 315 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7962 (mp) REVERT: B 432 GLU cc_start: 0.5747 (pt0) cc_final: 0.4919 (mt-10) REVERT: C 115 ASN cc_start: 0.8760 (m-40) cc_final: 0.8252 (m-40) REVERT: C 423 ASP cc_start: 0.5477 (p0) cc_final: 0.4956 (p0) REVERT: D 130 ARG cc_start: 0.6277 (ptp-110) cc_final: 0.5889 (ptp-170) REVERT: D 303 MET cc_start: 0.7962 (tpp) cc_final: 0.7665 (mmt) REVERT: D 443 MET cc_start: 0.6542 (tpp) cc_final: 0.6080 (mmm) REVERT: E 65 GLU cc_start: 0.6677 (tm-30) cc_final: 0.6218 (pt0) REVERT: E 179 ILE cc_start: 0.1413 (OUTLIER) cc_final: 0.1196 (pt) REVERT: E 379 ASP cc_start: 0.6432 (m-30) cc_final: 0.5753 (t70) REVERT: F 112 GLU cc_start: 0.7249 (mp0) cc_final: 0.7013 (pm20) REVERT: F 168 MET cc_start: -0.0125 (ptt) cc_final: -0.1063 (mpp) REVERT: F 353 ARG cc_start: 0.7651 (ptt180) cc_final: 0.7396 (ptt90) REVERT: F 360 THR cc_start: 0.8691 (t) cc_final: 0.8489 (p) REVERT: G 44 ASN cc_start: 0.5039 (m-40) cc_final: 0.4608 (t0) REVERT: G 310 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6508 (mp0) REVERT: G 345 THR cc_start: 0.8098 (t) cc_final: 0.7748 (p) REVERT: G 391 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6181 (mt) REVERT: G 400 LYS cc_start: 0.5494 (mmmm) cc_final: 0.5165 (mmtp) REVERT: H 39 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.5111 (mt) REVERT: H 118 ARG cc_start: 0.6930 (mtt-85) cc_final: 0.6404 (mtp85) REVERT: H 352 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7165 (mm) REVERT: H 391 LEU cc_start: 0.5686 (OUTLIER) cc_final: 0.5152 (mt) REVERT: H 402 THR cc_start: 0.8542 (t) cc_final: 0.8234 (m) REVERT: H 432 GLU cc_start: 0.5686 (mm-30) cc_final: 0.4911 (tt0) REVERT: I 247 ASN cc_start: 0.6450 (m-40) cc_final: 0.6101 (m-40) REVERT: I 275 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.4761 (tp) REVERT: I 295 VAL cc_start: 0.6582 (p) cc_final: 0.6259 (p) REVERT: I 360 ILE cc_start: 0.7995 (tt) cc_final: 0.7646 (mt) REVERT: I 363 THR cc_start: 0.8720 (m) cc_final: 0.8351 (p) REVERT: I 441 LYS cc_start: 0.7092 (tppt) cc_final: 0.6368 (mttp) REVERT: J 129 VAL cc_start: 0.5493 (t) cc_final: 0.5152 (p) REVERT: J 134 GLU cc_start: 0.3741 (OUTLIER) cc_final: 0.3025 (tt0) REVERT: J 178 MET cc_start: -0.0245 (mmp) cc_final: -0.0611 (ptm) REVERT: J 179 ILE cc_start: 0.1705 (OUTLIER) cc_final: 0.1147 (tp) REVERT: J 244 LEU cc_start: 0.7084 (mt) cc_final: 0.6866 (mt) REVERT: J 291 ILE cc_start: 0.5888 (mp) cc_final: 0.5294 (tt) REVERT: J 314 ARG cc_start: 0.7089 (tpp-160) cc_final: 0.6582 (tpt170) REVERT: J 415 LYS cc_start: 0.5115 (OUTLIER) cc_final: 0.3962 (tptt) REVERT: J 437 SER cc_start: 0.7547 (t) cc_final: 0.7239 (t) REVERT: J 441 GLN cc_start: 0.6829 (tm-30) cc_final: 0.6122 (pt0) REVERT: K 46 MET cc_start: 0.4457 (mtp) cc_final: 0.4123 (mtp) REVERT: K 168 MET cc_start: 0.0851 (OUTLIER) cc_final: -0.1221 (mtp) REVERT: K 171 ILE cc_start: 0.1622 (OUTLIER) cc_final: 0.0910 (tt) REVERT: K 288 LYS cc_start: 0.2555 (mmtm) cc_final: 0.2350 (tttm) REVERT: K 388 THR cc_start: 0.6493 (p) cc_final: 0.5906 (t) REVERT: L 41 GLN cc_start: 0.5551 (tm-30) cc_final: 0.5281 (tp40) REVERT: L 147 ILE cc_start: 0.0698 (OUTLIER) cc_final: 0.0297 (mt) REVERT: L 168 MET cc_start: 0.1057 (mmm) cc_final: 0.0521 (mtp) REVERT: L 358 SER cc_start: 0.7492 (p) cc_final: 0.7046 (t) REVERT: L 437 SER cc_start: 0.7540 (m) cc_final: 0.7196 (m) outliers start: 262 outliers final: 154 residues processed: 646 average time/residue: 0.2331 time to fit residues: 246.3059 Evaluate side-chains 541 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 369 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 442 TYR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 164 LYS Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 353 ASP Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 446 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 352 LEU Chi-restraints excluded: chain H residue 391 LEU Chi-restraints excluded: chain H residue 411 THR Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 335 ASN Chi-restraints excluded: chain I residue 337 VAL Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 367 THR Chi-restraints excluded: chain I residue 433 ILE Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 283 TRP Chi-restraints excluded: chain J residue 358 SER Chi-restraints excluded: chain J residue 362 TYR Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 415 LYS Chi-restraints excluded: chain J residue 426 ILE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 168 MET Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain K residue 419 THR Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 257 PHE Chi-restraints excluded: chain L residue 276 ILE Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 362 TYR Chi-restraints excluded: chain L residue 364 GLU Chi-restraints excluded: chain L residue 379 ASP Chi-restraints excluded: chain L residue 426 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 413 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 252 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS A 280 ASN ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN G 392 ASN G 393 HIS H 316 HIS H 335 ASN H 420 ASN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.226605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.216792 restraints weight = 42883.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.194874 restraints weight = 88967.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.187736 restraints weight = 89765.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.186770 restraints weight = 91842.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.186562 restraints weight = 77193.920| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3914 r_free = 0.3914 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3914 r_free = 0.3914 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37712 Z= 0.133 Angle : 0.623 8.525 50863 Z= 0.305 Chirality : 0.044 0.204 6040 Planarity : 0.004 0.051 6444 Dihedral : 9.085 174.968 5286 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.14 % Favored : 94.76 % Rotamer: Outliers : 6.60 % Allowed : 26.90 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.12), residues: 4693 helix: 1.13 (0.11), residues: 2156 sheet: -1.52 (0.19), residues: 653 loop : -1.65 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 400 TYR 0.021 0.001 TYR A 131 PHE 0.014 0.001 PHE D 257 TRP 0.032 0.004 TRP J 283 HIS 0.012 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00297 (37712) covalent geometry : angle 0.62334 (50863) hydrogen bonds : bond 0.03504 ( 1808) hydrogen bonds : angle 4.74162 ( 5175) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 391 time to evaluate : 1.329 Fit side-chains TARDY: cannot create tardy model for: "ASP A 449 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7119 (tp30) cc_final: 0.6836 (tp30) REVERT: A 371 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.7048 (tpp) REVERT: A 384 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7782 (mt) REVERT: B 64 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7544 (mtt180) REVERT: B 285 LYS cc_start: 0.6249 (OUTLIER) cc_final: 0.6008 (ttpp) REVERT: B 315 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7978 (mp) REVERT: C 115 ASN cc_start: 0.8740 (m-40) cc_final: 0.8213 (m-40) REVERT: C 281 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6699 (mtpt) REVERT: C 285 LYS cc_start: 0.6930 (mptt) cc_final: 0.6655 (mmtt) REVERT: C 423 ASP cc_start: 0.5505 (p0) cc_final: 0.4963 (p0) REVERT: D 130 ARG cc_start: 0.6171 (ptp-110) cc_final: 0.5776 (ptp-170) REVERT: D 303 MET cc_start: 0.8057 (tpp) cc_final: 0.7698 (mmt) REVERT: D 417 LYS cc_start: 0.6887 (mmmt) cc_final: 0.6142 (mtmm) REVERT: D 443 MET cc_start: 0.6559 (tpp) cc_final: 0.6182 (mmm) REVERT: E 179 ILE cc_start: 0.1387 (OUTLIER) cc_final: 0.1101 (pt) REVERT: E 350 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8148 (tt) REVERT: E 379 ASP cc_start: 0.6196 (m-30) cc_final: 0.5908 (t70) REVERT: F 33 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6329 (pp) REVERT: F 168 MET cc_start: 0.0036 (ptt) cc_final: -0.1523 (mtt) REVERT: F 353 ARG cc_start: 0.7769 (ptt180) cc_final: 0.7275 (ptt180) REVERT: G 44 ASN cc_start: 0.5107 (m-40) cc_final: 0.4714 (t0) REVERT: G 310 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6419 (mp0) REVERT: G 327 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7938 (m) REVERT: G 345 THR cc_start: 0.8024 (t) cc_final: 0.7765 (p) REVERT: G 391 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6076 (mt) REVERT: G 400 LYS cc_start: 0.5513 (mmmm) cc_final: 0.5292 (mmtp) REVERT: G 435 GLU cc_start: 0.7530 (tp30) cc_final: 0.6974 (tp30) REVERT: H 39 LEU cc_start: 0.5579 (OUTLIER) cc_final: 0.5243 (mt) REVERT: H 113 MET cc_start: 0.6013 (mtp) cc_final: 0.5717 (mtm) REVERT: H 118 ARG cc_start: 0.6964 (mtt-85) cc_final: 0.6413 (mtp85) REVERT: H 352 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7066 (mm) REVERT: H 391 LEU cc_start: 0.5583 (tp) cc_final: 0.5218 (mt) REVERT: H 432 GLU cc_start: 0.5697 (mm-30) cc_final: 0.5041 (tt0) REVERT: I 247 ASN cc_start: 0.6393 (m-40) cc_final: 0.6036 (m-40) REVERT: I 275 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.4759 (tp) REVERT: I 360 ILE cc_start: 0.8078 (tt) cc_final: 0.7771 (mt) REVERT: I 441 LYS cc_start: 0.7126 (tppt) cc_final: 0.6429 (mttp) REVERT: J 46 MET cc_start: 0.6082 (tpp) cc_final: 0.5131 (tpt) REVERT: J 60 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.7030 (mm) REVERT: J 134 GLU cc_start: 0.3948 (OUTLIER) cc_final: 0.2959 (tt0) REVERT: J 168 MET cc_start: 0.4357 (mtt) cc_final: 0.2425 (ptp) REVERT: J 179 ILE cc_start: 0.1413 (OUTLIER) cc_final: 0.0932 (tp) REVERT: J 244 LEU cc_start: 0.7046 (mt) cc_final: 0.6819 (mt) REVERT: J 291 ILE cc_start: 0.6274 (mp) cc_final: 0.5732 (tt) REVERT: J 310 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.8000 (m) REVERT: J 314 ARG cc_start: 0.7125 (tpp-160) cc_final: 0.6743 (tpt170) REVERT: J 415 LYS cc_start: 0.4899 (OUTLIER) cc_final: 0.3916 (tptt) REVERT: J 437 SER cc_start: 0.7523 (t) cc_final: 0.7207 (t) REVERT: J 441 GLN cc_start: 0.6809 (tm-30) cc_final: 0.6149 (pt0) REVERT: K 46 MET cc_start: 0.4689 (mtp) cc_final: 0.4225 (mtp) REVERT: K 168 MET cc_start: 0.0782 (OUTLIER) cc_final: -0.1175 (mtp) REVERT: K 288 LYS cc_start: 0.3093 (mmtm) cc_final: 0.2653 (tttt) REVERT: K 360 THR cc_start: 0.6822 (OUTLIER) cc_final: 0.6437 (p) REVERT: K 388 THR cc_start: 0.6776 (p) cc_final: 0.6232 (t) REVERT: K 442 TYR cc_start: 0.4407 (t80) cc_final: 0.4170 (t80) REVERT: L 71 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6884 (ttm170) REVERT: L 147 ILE cc_start: 0.0468 (OUTLIER) cc_final: 0.0082 (mt) REVERT: L 160 LYS cc_start: 0.1788 (OUTLIER) cc_final: 0.0366 (pttp) REVERT: L 168 MET cc_start: 0.1348 (mmm) cc_final: 0.0853 (mtm) REVERT: L 358 SER cc_start: 0.7430 (p) cc_final: 0.7007 (t) REVERT: L 414 ARG cc_start: 0.6567 (mtm110) cc_final: 0.6050 (mpt180) outliers start: 267 outliers final: 176 residues processed: 624 average time/residue: 0.2090 time to fit residues: 216.0811 Evaluate side-chains 543 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 344 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 442 TYR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 164 LYS Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 113 MET Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 353 ASP Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 335 ASN Chi-restraints excluded: chain H residue 352 LEU Chi-restraints excluded: chain H residue 411 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 335 ASN Chi-restraints excluded: chain I residue 337 VAL Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 367 THR Chi-restraints excluded: chain I residue 433 ILE Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 310 SER Chi-restraints excluded: chain J residue 332 ILE Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 352 ASP Chi-restraints excluded: chain J residue 358 SER Chi-restraints excluded: chain J residue 362 TYR Chi-restraints excluded: chain J residue 379 ASP Chi-restraints excluded: chain J residue 415 LYS Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain J residue 442 TYR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 168 MET Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 328 THR Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 357 VAL Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain K residue 419 THR Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 431 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 67 LYS Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 257 PHE Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 364 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 465 optimal weight: 6.9990 chunk 355 optimal weight: 5.9990 chunk 368 optimal weight: 8.9990 chunk 179 optimal weight: 0.9980 chunk 459 optimal weight: 3.9990 chunk 334 optimal weight: 20.0000 chunk 38 optimal weight: 0.5980 chunk 349 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 463 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 HIS D 146 GLN E 369 GLN F 404 GLN G 316 HIS G 392 ASN G 393 HIS H 20 HIS I 42 GLN ** I 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.223570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.213166 restraints weight = 42850.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.195281 restraints weight = 102767.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.188422 restraints weight = 88045.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.187099 restraints weight = 80348.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.186980 restraints weight = 67070.254| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3967 r_free = 0.3967 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| r_final: 0.3967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 37712 Z= 0.161 Angle : 0.637 7.774 50863 Z= 0.311 Chirality : 0.045 0.311 6040 Planarity : 0.005 0.068 6444 Dihedral : 8.737 175.344 5277 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.06 % Rotamer: Outliers : 7.56 % Allowed : 26.14 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.12), residues: 4693 helix: 1.07 (0.11), residues: 2151 sheet: -1.45 (0.19), residues: 640 loop : -1.66 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 400 TYR 0.026 0.002 TYR K 442 PHE 0.014 0.002 PHE D 257 TRP 0.079 0.005 TRP J 283 HIS 0.008 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00377 (37712) covalent geometry : angle 0.63726 (50863) hydrogen bonds : bond 0.03675 ( 1808) hydrogen bonds : angle 4.65018 ( 5175) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 306 poor density : 369 time to evaluate : 1.229 Fit side-chains TARDY: cannot create tardy model for: "ASP A 449 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 TYR cc_start: 0.3872 (OUTLIER) cc_final: 0.3519 (m-80) REVERT: A 233 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.4640 (mt-10) REVERT: A 384 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7595 (mp) REVERT: B 107 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6826 (mtmm) REVERT: B 247 ASN cc_start: 0.5115 (m110) cc_final: 0.4525 (t0) REVERT: B 279 ILE cc_start: 0.7610 (mm) cc_final: 0.7288 (mm) REVERT: B 285 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.6030 (ttpp) REVERT: B 315 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7947 (mp) REVERT: B 451 GLN cc_start: 0.3441 (OUTLIER) cc_final: 0.3094 (mt0) REVERT: C 18 HIS cc_start: 0.8911 (OUTLIER) cc_final: 0.8148 (m170) REVERT: C 115 ASN cc_start: 0.8856 (m-40) cc_final: 0.8325 (m-40) REVERT: C 281 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6701 (mtpt) REVERT: C 285 LYS cc_start: 0.6982 (mptt) cc_final: 0.6706 (mmtt) REVERT: C 423 ASP cc_start: 0.5651 (p0) cc_final: 0.5020 (p0) REVERT: D 130 ARG cc_start: 0.6390 (ptp-110) cc_final: 0.5979 (ptp-170) REVERT: D 146 GLN cc_start: 0.1129 (OUTLIER) cc_final: -0.0545 (tt0) REVERT: D 303 MET cc_start: 0.8083 (tpp) cc_final: 0.7734 (mmt) REVERT: D 378 GLU cc_start: 0.6310 (mm-30) cc_final: 0.5943 (mt-10) REVERT: D 442 TYR cc_start: 0.6222 (m-80) cc_final: 0.5996 (m-80) REVERT: E 71 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7636 (mtp180) REVERT: E 179 ILE cc_start: 0.1356 (OUTLIER) cc_final: 0.1042 (pt) REVERT: E 348 ILE cc_start: 0.7565 (mm) cc_final: 0.7361 (mm) REVERT: E 356 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8282 (mt) REVERT: F 33 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6421 (pp) REVERT: F 168 MET cc_start: 0.0456 (ptt) cc_final: -0.1385 (mtt) REVERT: G 44 ASN cc_start: 0.5147 (m-40) cc_final: 0.4847 (t0) REVERT: G 327 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7968 (m) REVERT: G 345 THR cc_start: 0.8249 (t) cc_final: 0.7914 (p) REVERT: G 391 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6010 (mt) REVERT: G 409 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.6206 (tt) REVERT: H 39 LEU cc_start: 0.5637 (OUTLIER) cc_final: 0.5316 (mt) REVERT: H 86 GLU cc_start: 0.5657 (mt-10) cc_final: 0.5234 (tt0) REVERT: H 113 MET cc_start: 0.6146 (mtp) cc_final: 0.5836 (mtm) REVERT: H 118 ARG cc_start: 0.6939 (mtt-85) cc_final: 0.6322 (mtp85) REVERT: H 352 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7060 (mm) REVERT: H 391 LEU cc_start: 0.5530 (tp) cc_final: 0.5257 (mt) REVERT: H 432 GLU cc_start: 0.5340 (mm-30) cc_final: 0.4923 (tt0) REVERT: I 247 ASN cc_start: 0.6450 (m-40) cc_final: 0.6212 (m-40) REVERT: I 360 ILE cc_start: 0.8184 (tt) cc_final: 0.7864 (mt) REVERT: I 384 ILE cc_start: 0.5412 (OUTLIER) cc_final: 0.5148 (mp) REVERT: I 388 GLU cc_start: 0.4030 (mm-30) cc_final: 0.3150 (tm-30) REVERT: I 441 LYS cc_start: 0.7199 (tppt) cc_final: 0.6495 (mttp) REVERT: J 134 GLU cc_start: 0.3518 (OUTLIER) cc_final: 0.2647 (tt0) REVERT: J 168 MET cc_start: 0.4492 (mtt) cc_final: 0.2652 (ptp) REVERT: J 179 ILE cc_start: 0.1567 (OUTLIER) cc_final: 0.1031 (tp) REVERT: J 244 LEU cc_start: 0.7208 (mt) cc_final: 0.6994 (mt) REVERT: J 291 ILE cc_start: 0.6142 (mp) cc_final: 0.5620 (tt) REVERT: J 310 SER cc_start: 0.8485 (OUTLIER) cc_final: 0.8017 (m) REVERT: J 415 LYS cc_start: 0.5106 (OUTLIER) cc_final: 0.3982 (tptt) REVERT: J 441 GLN cc_start: 0.6797 (tm-30) cc_final: 0.6109 (pt0) REVERT: K 50 LEU cc_start: 0.5888 (OUTLIER) cc_final: 0.5545 (mt) REVERT: K 168 MET cc_start: 0.0986 (OUTLIER) cc_final: -0.1072 (mtp) REVERT: K 288 LYS cc_start: 0.3170 (mmtm) cc_final: 0.2748 (tttt) REVERT: K 360 THR cc_start: 0.6893 (OUTLIER) cc_final: 0.6584 (p) REVERT: K 388 THR cc_start: 0.6709 (p) cc_final: 0.6180 (t) REVERT: L 71 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6829 (mtm180) REVERT: L 147 ILE cc_start: 0.0715 (OUTLIER) cc_final: 0.0178 (mt) REVERT: L 160 LYS cc_start: 0.2010 (OUTLIER) cc_final: 0.0327 (pttp) REVERT: L 168 MET cc_start: 0.1298 (mmm) cc_final: 0.1042 (mtm) REVERT: L 358 SER cc_start: 0.7509 (p) cc_final: 0.7047 (t) REVERT: L 414 ARG cc_start: 0.6605 (mtm110) cc_final: 0.6187 (mpt180) outliers start: 306 outliers final: 204 residues processed: 638 average time/residue: 0.2103 time to fit residues: 222.1751 Evaluate side-chains 572 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 338 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 388 THR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 442 TYR Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 164 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 353 ASP Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 295 VAL Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain H residue 352 LEU Chi-restraints excluded: chain H residue 411 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 335 ASN Chi-restraints excluded: chain I residue 337 VAL Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 367 THR Chi-restraints excluded: chain I residue 380 GLN Chi-restraints excluded: chain I residue 384 ILE Chi-restraints excluded: chain I residue 433 ILE Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 310 SER Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 332 ILE Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 352 ASP Chi-restraints excluded: chain J residue 358 SER Chi-restraints excluded: chain J residue 362 TYR Chi-restraints excluded: chain J residue 379 ASP Chi-restraints excluded: chain J residue 415 LYS Chi-restraints excluded: chain J residue 426 ILE Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 168 MET Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 338 THR Chi-restraints excluded: chain K residue 346 ILE Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 357 VAL Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain K residue 419 THR Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 431 SER Chi-restraints excluded: chain K residue 437 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 67 LYS Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 172 TYR Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 349 ASP Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 364 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 407 optimal weight: 20.0000 chunk 240 optimal weight: 2.9990 chunk 395 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 404 optimal weight: 8.9990 chunk 473 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN D 146 GLN ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN G 392 ASN G 393 HIS ** H 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.221732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.211114 restraints weight = 42739.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.193879 restraints weight = 101757.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.187055 restraints weight = 92376.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.184741 restraints weight = 75754.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.184765 restraints weight = 67932.281| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| r_final: 0.3913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 37712 Z= 0.184 Angle : 0.667 9.023 50863 Z= 0.327 Chirality : 0.046 0.225 6040 Planarity : 0.005 0.064 6444 Dihedral : 8.630 176.805 5270 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.35 % Favored : 94.52 % Rotamer: Outliers : 7.36 % Allowed : 26.19 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.12), residues: 4693 helix: 0.95 (0.11), residues: 2147 sheet: -1.55 (0.19), residues: 659 loop : -1.64 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 64 TYR 0.023 0.002 TYR G 102 PHE 0.014 0.002 PHE D 257 TRP 0.050 0.005 TRP J 283 HIS 0.010 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00439 (37712) covalent geometry : angle 0.66665 (50863) hydrogen bonds : bond 0.03835 ( 1808) hydrogen bonds : angle 4.65241 ( 5175) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 298 poor density : 350 time to evaluate : 1.458 Fit side-chains TARDY: cannot create tardy model for: "ASP A 449 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 TYR cc_start: 0.3799 (OUTLIER) cc_final: 0.3487 (m-80) REVERT: A 233 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.4809 (mt-10) REVERT: A 384 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7698 (mp) REVERT: B 12 THR cc_start: 0.7914 (m) cc_final: 0.7642 (p) REVERT: B 105 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7399 (pm20) REVERT: B 107 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7109 (ptmm) REVERT: B 279 ILE cc_start: 0.7720 (mm) cc_final: 0.7488 (mm) REVERT: B 285 LYS cc_start: 0.6208 (OUTLIER) cc_final: 0.5983 (ttpp) REVERT: B 315 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7936 (mp) REVERT: B 451 GLN cc_start: 0.3550 (OUTLIER) cc_final: 0.3158 (mt0) REVERT: C 18 HIS cc_start: 0.8909 (OUTLIER) cc_final: 0.8666 (m90) REVERT: C 115 ASN cc_start: 0.8919 (m-40) cc_final: 0.8438 (m-40) REVERT: C 423 ASP cc_start: 0.5675 (p0) cc_final: 0.5023 (p0) REVERT: D 442 TYR cc_start: 0.6173 (m-80) cc_final: 0.5953 (m-80) REVERT: E 71 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7696 (mtp180) REVERT: E 168 MET cc_start: 0.2904 (tmm) cc_final: 0.1948 (ttt) REVERT: E 179 ILE cc_start: 0.1504 (OUTLIER) cc_final: 0.1170 (pt) REVERT: E 348 ILE cc_start: 0.7621 (mm) cc_final: 0.7369 (mm) REVERT: E 356 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8239 (mt) REVERT: F 168 MET cc_start: 0.0769 (ptt) cc_final: -0.0881 (mtt) REVERT: G 44 ASN cc_start: 0.5290 (m-40) cc_final: 0.5082 (t0) REVERT: G 391 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6099 (mt) REVERT: G 435 GLU cc_start: 0.7450 (tp30) cc_final: 0.7042 (tp30) REVERT: H 39 LEU cc_start: 0.5717 (OUTLIER) cc_final: 0.5343 (mt) REVERT: H 86 GLU cc_start: 0.5840 (mt-10) cc_final: 0.5270 (tt0) REVERT: H 111 VAL cc_start: 0.6971 (OUTLIER) cc_final: 0.6436 (t) REVERT: H 113 MET cc_start: 0.6255 (mtp) cc_final: 0.5887 (mtm) REVERT: H 118 ARG cc_start: 0.7085 (mtt-85) cc_final: 0.6381 (mtp85) REVERT: H 352 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7093 (mm) REVERT: H 418 LYS cc_start: 0.6871 (mmpt) cc_final: 0.6046 (mtmt) REVERT: H 432 GLU cc_start: 0.5309 (mm-30) cc_final: 0.4911 (tt0) REVERT: I 13 GLN cc_start: 0.5021 (pm20) cc_final: 0.4461 (pt0) REVERT: I 216 GLU cc_start: 0.1073 (OUTLIER) cc_final: 0.0569 (mm-30) REVERT: I 247 ASN cc_start: 0.6512 (m-40) cc_final: 0.6279 (m-40) REVERT: I 360 ILE cc_start: 0.8133 (tt) cc_final: 0.7911 (mt) REVERT: I 384 ILE cc_start: 0.5527 (OUTLIER) cc_final: 0.5248 (mp) REVERT: I 388 GLU cc_start: 0.4018 (mm-30) cc_final: 0.3174 (tm-30) REVERT: J 134 GLU cc_start: 0.3470 (OUTLIER) cc_final: 0.2550 (tt0) REVERT: J 168 MET cc_start: 0.4482 (mtt) cc_final: 0.2688 (ptp) REVERT: J 179 ILE cc_start: 0.1562 (OUTLIER) cc_final: 0.1012 (tp) REVERT: J 291 ILE cc_start: 0.6117 (mp) cc_final: 0.5570 (tt) REVERT: J 310 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8021 (m) REVERT: J 415 LYS cc_start: 0.5146 (OUTLIER) cc_final: 0.3991 (tptt) REVERT: J 436 GLU cc_start: 0.5009 (OUTLIER) cc_final: 0.4545 (pt0) REVERT: J 441 GLN cc_start: 0.6786 (tm-30) cc_final: 0.6135 (pt0) REVERT: J 445 GLU cc_start: 0.6680 (mm-30) cc_final: 0.5999 (mt-10) REVERT: K 46 MET cc_start: 0.5267 (mtp) cc_final: 0.5026 (mtp) REVERT: K 50 LEU cc_start: 0.5847 (OUTLIER) cc_final: 0.5511 (mt) REVERT: K 168 MET cc_start: 0.1114 (OUTLIER) cc_final: -0.0997 (mtp) REVERT: K 288 LYS cc_start: 0.3425 (mmtm) cc_final: 0.2940 (tttt) REVERT: K 360 THR cc_start: 0.6954 (OUTLIER) cc_final: 0.6664 (p) REVERT: K 388 THR cc_start: 0.6809 (p) cc_final: 0.6320 (t) REVERT: L 71 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6931 (mtt180) REVERT: L 358 SER cc_start: 0.7652 (p) cc_final: 0.7209 (t) REVERT: L 414 ARG cc_start: 0.6654 (mtm110) cc_final: 0.6176 (mpt180) outliers start: 298 outliers final: 218 residues processed: 611 average time/residue: 0.2076 time to fit residues: 210.7511 Evaluate side-chains 574 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 329 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 388 THR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 442 TYR Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 164 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 353 ASP Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 295 VAL Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 352 LEU Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain H residue 411 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 335 ASN Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 367 THR Chi-restraints excluded: chain I residue 380 GLN Chi-restraints excluded: chain I residue 384 ILE Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain I residue 433 ILE Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 310 SER Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 332 ILE Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 352 ASP Chi-restraints excluded: chain J residue 358 SER Chi-restraints excluded: chain J residue 415 LYS Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain J residue 436 GLU Chi-restraints excluded: chain J residue 437 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 168 MET Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 338 THR Chi-restraints excluded: chain K residue 346 ILE Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 357 VAL Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain K residue 419 THR Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 431 SER Chi-restraints excluded: chain K residue 437 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 67 LYS Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 262 SER Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 349 ASP Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 437 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 280 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 452 optimal weight: 0.0970 chunk 267 optimal weight: 5.9990 chunk 461 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 251 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 312 optimal weight: 0.6980 chunk 185 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 GLN G 392 ASN G 393 HIS ** H 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.222877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.186850 restraints weight = 42907.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.180726 restraints weight = 59005.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.180305 restraints weight = 56945.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.180695 restraints weight = 57761.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.181213 restraints weight = 39443.806| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 37712 Z= 0.141 Angle : 0.617 10.086 50863 Z= 0.300 Chirality : 0.044 0.222 6040 Planarity : 0.004 0.054 6444 Dihedral : 8.323 171.961 5268 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.92 % Favored : 94.93 % Rotamer: Outliers : 6.18 % Allowed : 27.45 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.12), residues: 4693 helix: 1.05 (0.11), residues: 2152 sheet: -1.58 (0.19), residues: 656 loop : -1.55 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 64 TYR 0.018 0.001 TYR G 102 PHE 0.011 0.001 PHE D 257 TRP 0.039 0.004 TRP J 283 HIS 0.007 0.001 HIS G 393 Details of bonding type rmsd covalent geometry : bond 0.00328 (37712) covalent geometry : angle 0.61704 (50863) hydrogen bonds : bond 0.03434 ( 1808) hydrogen bonds : angle 4.49664 ( 5175) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 360 time to evaluate : 1.465 Fit side-chains TARDY: cannot create tardy model for: "ASP A 449 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 TYR cc_start: 0.4080 (OUTLIER) cc_final: 0.3790 (m-80) REVERT: A 281 LYS cc_start: 0.6988 (mmtt) cc_final: 0.6629 (mtmt) REVERT: A 288 ASP cc_start: 0.5386 (m-30) cc_final: 0.4623 (t70) REVERT: A 384 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7791 (mt) REVERT: B 6 VAL cc_start: 0.6997 (OUTLIER) cc_final: 0.6737 (t) REVERT: B 12 THR cc_start: 0.7879 (m) cc_final: 0.7627 (p) REVERT: B 107 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.6833 (mtmm) REVERT: B 279 ILE cc_start: 0.7722 (mm) cc_final: 0.7434 (mm) REVERT: B 285 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5939 (ttpp) REVERT: B 315 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7897 (mp) REVERT: B 408 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7258 (pt0) REVERT: B 451 GLN cc_start: 0.3669 (OUTLIER) cc_final: 0.3238 (mt0) REVERT: C 18 HIS cc_start: 0.8879 (OUTLIER) cc_final: 0.8130 (m170) REVERT: C 115 ASN cc_start: 0.8869 (m-40) cc_final: 0.8373 (m-40) REVERT: C 423 ASP cc_start: 0.5717 (p0) cc_final: 0.5070 (p0) REVERT: C 426 GLU cc_start: 0.6246 (mm-30) cc_final: 0.5855 (mm-30) REVERT: D 441 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6487 (tt0) REVERT: D 442 TYR cc_start: 0.6170 (m-80) cc_final: 0.5749 (m-10) REVERT: E 71 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7636 (mtp180) REVERT: E 168 MET cc_start: 0.2372 (tmm) cc_final: 0.1546 (ttt) REVERT: E 179 ILE cc_start: 0.1374 (OUTLIER) cc_final: 0.1016 (pt) REVERT: E 348 ILE cc_start: 0.7617 (mm) cc_final: 0.7389 (mm) REVERT: E 356 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8317 (mt) REVERT: F 168 MET cc_start: 0.0474 (ptt) cc_final: -0.1149 (mtt) REVERT: G 391 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.5989 (mt) REVERT: G 435 GLU cc_start: 0.7540 (tp30) cc_final: 0.7170 (tp30) REVERT: H 39 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5315 (mt) REVERT: H 86 GLU cc_start: 0.5887 (mt-10) cc_final: 0.5314 (tt0) REVERT: H 113 MET cc_start: 0.6302 (mtp) cc_final: 0.5954 (mtm) REVERT: H 118 ARG cc_start: 0.7076 (mtt-85) cc_final: 0.6549 (mtp85) REVERT: H 352 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7058 (mm) REVERT: H 391 LEU cc_start: 0.5426 (mt) cc_final: 0.5178 (mt) REVERT: H 418 LYS cc_start: 0.6942 (mmpt) cc_final: 0.6039 (mtmt) REVERT: H 432 GLU cc_start: 0.5375 (mm-30) cc_final: 0.4942 (tt0) REVERT: I 13 GLN cc_start: 0.5094 (pm20) cc_final: 0.4619 (pt0) REVERT: I 247 ASN cc_start: 0.6523 (m-40) cc_final: 0.6319 (m110) REVERT: I 360 ILE cc_start: 0.8158 (tt) cc_final: 0.7853 (mt) REVERT: I 384 ILE cc_start: 0.5350 (OUTLIER) cc_final: 0.5098 (mp) REVERT: I 388 GLU cc_start: 0.4194 (mm-30) cc_final: 0.2538 (tm-30) REVERT: J 134 GLU cc_start: 0.3485 (OUTLIER) cc_final: 0.2471 (tt0) REVERT: J 168 MET cc_start: 0.4225 (mtt) cc_final: 0.2354 (ptp) REVERT: J 179 ILE cc_start: 0.1366 (OUTLIER) cc_final: 0.0911 (tp) REVERT: J 291 ILE cc_start: 0.6071 (mp) cc_final: 0.5694 (tt) REVERT: J 310 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.8035 (m) REVERT: J 380 VAL cc_start: 0.4093 (p) cc_final: 0.3831 (m) REVERT: J 415 LYS cc_start: 0.4855 (OUTLIER) cc_final: 0.3788 (tptt) REVERT: J 431 SER cc_start: 0.6607 (OUTLIER) cc_final: 0.6339 (m) REVERT: J 441 GLN cc_start: 0.6779 (tm-30) cc_final: 0.6152 (pt0) REVERT: J 445 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6074 (mt-10) REVERT: K 46 MET cc_start: 0.5193 (mtp) cc_final: 0.4942 (mtp) REVERT: K 50 LEU cc_start: 0.5899 (OUTLIER) cc_final: 0.5531 (mt) REVERT: K 168 MET cc_start: 0.0948 (OUTLIER) cc_final: -0.0983 (mtp) REVERT: K 288 LYS cc_start: 0.3622 (mmtm) cc_final: 0.2916 (tttt) REVERT: K 360 THR cc_start: 0.6908 (OUTLIER) cc_final: 0.6694 (p) REVERT: K 388 THR cc_start: 0.7030 (p) cc_final: 0.6508 (t) REVERT: L 71 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6829 (mtt180) REVERT: L 112 GLU cc_start: 0.6116 (mp0) cc_final: 0.5562 (mt-10) REVERT: L 160 LYS cc_start: 0.2012 (OUTLIER) cc_final: 0.0480 (pttp) REVERT: L 168 MET cc_start: 0.2557 (mmt) cc_final: 0.1788 (mtt) REVERT: L 203 SER cc_start: 0.3669 (OUTLIER) cc_final: 0.2936 (p) REVERT: L 358 SER cc_start: 0.7584 (p) cc_final: 0.7190 (t) REVERT: L 414 ARG cc_start: 0.6600 (mtm110) cc_final: 0.6044 (mpt180) outliers start: 250 outliers final: 189 residues processed: 583 average time/residue: 0.2072 time to fit residues: 201.4644 Evaluate side-chains 554 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 338 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 388 THR Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 442 TYR Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 164 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 295 VAL Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 352 LEU Chi-restraints excluded: chain H residue 411 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 335 ASN Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 367 THR Chi-restraints excluded: chain I residue 380 GLN Chi-restraints excluded: chain I residue 384 ILE Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain I residue 433 ILE Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 310 SER Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 332 ILE Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 352 ASP Chi-restraints excluded: chain J residue 358 SER Chi-restraints excluded: chain J residue 415 LYS Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 168 MET Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 338 THR Chi-restraints excluded: chain K residue 346 ILE Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 357 VAL Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 431 SER Chi-restraints excluded: chain K residue 437 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 67 LYS Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 437 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 145 optimal weight: 1.9990 chunk 321 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 311 optimal weight: 5.9990 chunk 460 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 458 optimal weight: 20.0000 chunk 471 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 392 ASN G 393 HIS ** H 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 245 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.219714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.211465 restraints weight = 42646.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.208852 restraints weight = 81052.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.192215 restraints weight = 107911.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.187458 restraints weight = 90746.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.184988 restraints weight = 68977.594| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3974 r_free = 0.3974 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3974 r_free = 0.3974 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.3974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 37712 Z= 0.193 Angle : 0.689 10.459 50863 Z= 0.335 Chirality : 0.046 0.252 6040 Planarity : 0.005 0.058 6444 Dihedral : 8.314 167.630 5266 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.26 % Favored : 94.57 % Rotamer: Outliers : 6.30 % Allowed : 27.22 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.12), residues: 4693 helix: 0.87 (0.11), residues: 2144 sheet: -1.58 (0.19), residues: 659 loop : -1.62 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 400 TYR 0.018 0.002 TYR B 192 PHE 0.012 0.002 PHE K 123 TRP 0.036 0.004 TRP E 283 HIS 0.009 0.002 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00460 (37712) covalent geometry : angle 0.68948 (50863) hydrogen bonds : bond 0.03941 ( 1808) hydrogen bonds : angle 4.59609 ( 5175) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 255 poor density : 353 time to evaluate : 1.534 Fit side-chains TARDY: cannot create tardy model for: "ASP A 449 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 TYR cc_start: 0.3666 (OUTLIER) cc_final: 0.3324 (m-80) REVERT: A 233 GLU cc_start: 0.6109 (OUTLIER) cc_final: 0.5013 (mt-10) REVERT: A 281 LYS cc_start: 0.7009 (mmtt) cc_final: 0.6609 (mttt) REVERT: A 288 ASP cc_start: 0.5352 (m-30) cc_final: 0.4594 (t70) REVERT: A 396 GLU cc_start: 0.7223 (pt0) cc_final: 0.6938 (mt-10) REVERT: B 6 VAL cc_start: 0.7221 (OUTLIER) cc_final: 0.6942 (t) REVERT: B 12 THR cc_start: 0.7940 (m) cc_final: 0.7669 (p) REVERT: B 105 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7555 (pm20) REVERT: B 107 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7147 (ptmm) REVERT: B 279 ILE cc_start: 0.7837 (mm) cc_final: 0.7579 (mm) REVERT: B 285 LYS cc_start: 0.6217 (OUTLIER) cc_final: 0.5981 (ttpp) REVERT: B 315 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7951 (mp) REVERT: B 396 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6290 (mp0) REVERT: B 451 GLN cc_start: 0.3665 (OUTLIER) cc_final: 0.3254 (mt0) REVERT: C 18 HIS cc_start: 0.8875 (OUTLIER) cc_final: 0.8013 (m170) REVERT: C 306 MET cc_start: 0.8201 (tpp) cc_final: 0.7996 (mmm) REVERT: C 423 ASP cc_start: 0.5897 (p0) cc_final: 0.5223 (p0) REVERT: C 426 GLU cc_start: 0.6293 (mm-30) cc_final: 0.6040 (tp30) REVERT: D 29 ARG cc_start: 0.6747 (OUTLIER) cc_final: 0.5817 (mtt-85) REVERT: D 441 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6555 (tt0) REVERT: D 442 TYR cc_start: 0.6254 (m-80) cc_final: 0.5879 (m-10) REVERT: E 71 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7712 (mtp180) REVERT: E 168 MET cc_start: 0.3081 (tmm) cc_final: 0.2063 (ttt) REVERT: E 179 ILE cc_start: 0.1063 (OUTLIER) cc_final: 0.0640 (pt) REVERT: E 348 ILE cc_start: 0.7701 (mm) cc_final: 0.7438 (mm) REVERT: E 356 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8276 (mt) REVERT: F 113 MET cc_start: 0.7432 (mtm) cc_final: 0.7153 (mtt) REVERT: F 168 MET cc_start: 0.1175 (ptt) cc_final: 0.0695 (ptt) REVERT: G 391 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6286 (mt) REVERT: H 39 LEU cc_start: 0.5816 (OUTLIER) cc_final: 0.5433 (mt) REVERT: H 86 GLU cc_start: 0.5658 (mt-10) cc_final: 0.5294 (tt0) REVERT: H 113 MET cc_start: 0.6362 (mtp) cc_final: 0.5981 (mtm) REVERT: H 118 ARG cc_start: 0.7135 (mtt-85) cc_final: 0.6491 (mtp85) REVERT: H 170 LEU cc_start: 0.1614 (OUTLIER) cc_final: 0.1270 (pt) REVERT: H 238 VAL cc_start: 0.6648 (m) cc_final: 0.6320 (p) REVERT: H 352 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7031 (mm) REVERT: H 391 LEU cc_start: 0.5479 (mt) cc_final: 0.5200 (mt) REVERT: H 418 LYS cc_start: 0.6954 (mmpt) cc_final: 0.6192 (mtmt) REVERT: H 432 GLU cc_start: 0.5167 (mm-30) cc_final: 0.4878 (tt0) REVERT: I 13 GLN cc_start: 0.5326 (pm20) cc_final: 0.4918 (pt0) REVERT: I 216 GLU cc_start: 0.0989 (OUTLIER) cc_final: 0.0478 (mm-30) REVERT: I 275 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6134 (pp) REVERT: I 360 ILE cc_start: 0.8134 (tt) cc_final: 0.7872 (mt) REVERT: I 384 ILE cc_start: 0.5628 (OUTLIER) cc_final: 0.5383 (mp) REVERT: I 388 GLU cc_start: 0.4045 (mm-30) cc_final: 0.2585 (tm-30) REVERT: J 168 MET cc_start: 0.4542 (mtt) cc_final: 0.2799 (ptp) REVERT: J 179 ILE cc_start: 0.1808 (OUTLIER) cc_final: 0.1218 (tp) REVERT: J 241 THR cc_start: 0.3191 (OUTLIER) cc_final: 0.2805 (t) REVERT: J 310 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8026 (m) REVERT: J 415 LYS cc_start: 0.5022 (OUTLIER) cc_final: 0.3902 (tptt) REVERT: J 436 GLU cc_start: 0.4956 (OUTLIER) cc_final: 0.4564 (pt0) REVERT: J 441 GLN cc_start: 0.6722 (tm-30) cc_final: 0.6055 (pt0) REVERT: J 445 GLU cc_start: 0.6645 (mm-30) cc_final: 0.6085 (mt-10) REVERT: K 46 MET cc_start: 0.5254 (mtp) cc_final: 0.5035 (mtp) REVERT: K 50 LEU cc_start: 0.5877 (OUTLIER) cc_final: 0.5521 (mt) REVERT: K 168 MET cc_start: 0.1418 (OUTLIER) cc_final: -0.0600 (mtp) REVERT: K 288 LYS cc_start: 0.3545 (mmtm) cc_final: 0.3100 (tttp) REVERT: K 360 THR cc_start: 0.7170 (OUTLIER) cc_final: 0.6957 (p) REVERT: L 71 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6814 (mtt180) REVERT: L 112 GLU cc_start: 0.6068 (mp0) cc_final: 0.5604 (mt-10) REVERT: L 143 VAL cc_start: 0.2456 (OUTLIER) cc_final: 0.2119 (p) REVERT: L 168 MET cc_start: 0.2547 (mmt) cc_final: 0.2108 (mtt) REVERT: L 203 SER cc_start: 0.4269 (OUTLIER) cc_final: 0.3667 (p) REVERT: L 358 SER cc_start: 0.7734 (p) cc_final: 0.7352 (t) REVERT: L 414 ARG cc_start: 0.6589 (mtm110) cc_final: 0.6202 (mpt180) outliers start: 255 outliers final: 199 residues processed: 582 average time/residue: 0.2039 time to fit residues: 197.6033 Evaluate side-chains 558 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 326 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 388 THR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 442 TYR Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 164 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 295 VAL Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 337 VAL Chi-restraints excluded: chain H residue 352 LEU Chi-restraints excluded: chain H residue 411 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 335 ASN Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 367 THR Chi-restraints excluded: chain I residue 380 GLN Chi-restraints excluded: chain I residue 384 ILE Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain I residue 433 ILE Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 143 VAL Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 310 SER Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 332 ILE Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 358 SER Chi-restraints excluded: chain J residue 415 LYS Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain J residue 436 GLU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 168 MET Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 203 SER Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 338 THR Chi-restraints excluded: chain K residue 346 ILE Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 357 VAL Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain K residue 419 THR Chi-restraints excluded: chain K residue 431 SER Chi-restraints excluded: chain K residue 437 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 437 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 245 optimal weight: 20.0000 chunk 373 optimal weight: 9.9990 chunk 180 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 297 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 407 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 451 optimal weight: 10.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 392 ASN G 393 HIS H 280 ASN ** H 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 451 GLN ** J 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.219384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.208460 restraints weight = 43107.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.206226 restraints weight = 80536.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.198711 restraints weight = 84067.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.194319 restraints weight = 87000.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.189534 restraints weight = 65903.410| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4050 r_free = 0.4050 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4050 r_free = 0.4050 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.4050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 37712 Z= 0.152 Angle : 0.633 12.272 50863 Z= 0.306 Chirality : 0.044 0.260 6040 Planarity : 0.004 0.057 6444 Dihedral : 7.913 170.991 5263 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.96 % Favored : 94.89 % Rotamer: Outliers : 5.73 % Allowed : 27.87 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.12), residues: 4693 helix: 0.95 (0.11), residues: 2155 sheet: -1.49 (0.19), residues: 670 loop : -1.57 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 64 TYR 0.017 0.002 TYR B 192 PHE 0.011 0.001 PHE D 257 TRP 0.036 0.004 TRP E 283 HIS 0.007 0.001 HIS G 393 Details of bonding type rmsd covalent geometry : bond 0.00359 (37712) covalent geometry : angle 0.63272 (50863) hydrogen bonds : bond 0.03548 ( 1808) hydrogen bonds : angle 4.49513 ( 5175) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 352 time to evaluate : 1.152 Fit side-chains TARDY: cannot create tardy model for: "ASP A 449 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 449 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 209 TYR cc_start: 0.3518 (OUTLIER) cc_final: 0.3197 (m-80) REVERT: A 233 GLU cc_start: 0.6158 (OUTLIER) cc_final: 0.5115 (mt-10) REVERT: A 281 LYS cc_start: 0.7026 (mmtt) cc_final: 0.6633 (mttt) REVERT: A 396 GLU cc_start: 0.7203 (pt0) cc_final: 0.6926 (mt-10) REVERT: B 107 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7064 (ptmm) REVERT: B 279 ILE cc_start: 0.7777 (mm) cc_final: 0.7522 (mm) REVERT: B 285 LYS cc_start: 0.6121 (OUTLIER) cc_final: 0.5876 (ttpp) REVERT: B 315 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7915 (mp) REVERT: B 408 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7210 (pt0) REVERT: B 451 GLN cc_start: 0.3741 (OUTLIER) cc_final: 0.3329 (mt0) REVERT: C 115 ASN cc_start: 0.8884 (m-40) cc_final: 0.8427 (m-40) REVERT: C 306 MET cc_start: 0.8152 (tpp) cc_final: 0.7920 (mmm) REVERT: C 342 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.5655 (pt0) REVERT: C 423 ASP cc_start: 0.5921 (p0) cc_final: 0.5247 (p0) REVERT: C 426 GLU cc_start: 0.6387 (mm-30) cc_final: 0.6142 (tp30) REVERT: D 29 ARG cc_start: 0.6564 (OUTLIER) cc_final: 0.5796 (mtt-85) REVERT: D 441 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6650 (tt0) REVERT: D 442 TYR cc_start: 0.6204 (m-80) cc_final: 0.5883 (m-10) REVERT: E 168 MET cc_start: 0.3235 (tmm) cc_final: 0.2147 (ttt) REVERT: E 179 ILE cc_start: 0.1033 (OUTLIER) cc_final: 0.0638 (pt) REVERT: E 348 ILE cc_start: 0.7666 (mm) cc_final: 0.7408 (mm) REVERT: E 356 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8273 (mt) REVERT: F 90 MET cc_start: 0.7805 (mtp) cc_final: 0.7548 (mtp) REVERT: F 113 MET cc_start: 0.7363 (mtm) cc_final: 0.7138 (mtt) REVERT: F 168 MET cc_start: 0.1277 (ptt) cc_final: 0.0906 (ptt) REVERT: G 114 GLU cc_start: 0.6882 (tp30) cc_final: 0.6585 (tt0) REVERT: G 280 ASN cc_start: 0.4874 (OUTLIER) cc_final: 0.4581 (m-40) REVERT: G 391 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6323 (mt) REVERT: H 39 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5431 (mt) REVERT: H 86 GLU cc_start: 0.5549 (mt-10) cc_final: 0.5282 (tp30) REVERT: H 113 MET cc_start: 0.6400 (mtp) cc_final: 0.6032 (mtm) REVERT: H 170 LEU cc_start: 0.1743 (OUTLIER) cc_final: 0.1380 (pt) REVERT: H 352 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7047 (mm) REVERT: H 391 LEU cc_start: 0.5472 (mt) cc_final: 0.5207 (mt) REVERT: H 418 LYS cc_start: 0.6883 (mmpt) cc_final: 0.6253 (mtmt) REVERT: I 13 GLN cc_start: 0.5410 (pm20) cc_final: 0.4981 (pt0) REVERT: I 360 ILE cc_start: 0.8079 (tt) cc_final: 0.7783 (mt) REVERT: I 384 ILE cc_start: 0.5690 (OUTLIER) cc_final: 0.5440 (mp) REVERT: I 388 GLU cc_start: 0.4022 (mm-30) cc_final: 0.2691 (tm-30) REVERT: J 168 MET cc_start: 0.4655 (mtt) cc_final: 0.3030 (ptp) REVERT: J 179 ILE cc_start: 0.1965 (OUTLIER) cc_final: 0.1323 (tp) REVERT: J 241 THR cc_start: 0.3063 (OUTLIER) cc_final: 0.2664 (t) REVERT: J 310 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8052 (m) REVERT: J 415 LYS cc_start: 0.5010 (OUTLIER) cc_final: 0.3780 (tptm) REVERT: J 436 GLU cc_start: 0.4936 (OUTLIER) cc_final: 0.4692 (pt0) REVERT: J 441 GLN cc_start: 0.6644 (tm-30) cc_final: 0.6120 (pt0) REVERT: J 445 GLU cc_start: 0.6451 (mm-30) cc_final: 0.6080 (mt-10) REVERT: K 50 LEU cc_start: 0.5791 (OUTLIER) cc_final: 0.5438 (mt) REVERT: K 168 MET cc_start: 0.1394 (OUTLIER) cc_final: -0.0507 (mtp) REVERT: L 71 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6666 (mtt180) REVERT: L 112 GLU cc_start: 0.6030 (mp0) cc_final: 0.5529 (mt-10) REVERT: L 168 MET cc_start: 0.2424 (mmt) cc_final: 0.2120 (mtt) REVERT: L 203 SER cc_start: 0.4374 (OUTLIER) cc_final: 0.3823 (p) REVERT: L 358 SER cc_start: 0.7813 (p) cc_final: 0.7435 (t) REVERT: L 414 ARG cc_start: 0.6492 (mtm110) cc_final: 0.6257 (mpt180) outliers start: 232 outliers final: 187 residues processed: 562 average time/residue: 0.2162 time to fit residues: 202.2979 Evaluate side-chains 543 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 330 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 388 THR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 442 TYR Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 164 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain G residue 435 GLU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 352 LEU Chi-restraints excluded: chain H residue 411 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 335 ASN Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 367 THR Chi-restraints excluded: chain I residue 380 GLN Chi-restraints excluded: chain I residue 384 ILE Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain I residue 433 ILE Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 310 SER Chi-restraints excluded: chain J residue 332 ILE Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 358 SER Chi-restraints excluded: chain J residue 415 LYS Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain J residue 436 GLU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 168 MET Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 338 THR Chi-restraints excluded: chain K residue 346 ILE Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 357 VAL Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain K residue 431 SER Chi-restraints excluded: chain K residue 437 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 437 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 372 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 391 optimal weight: 20.0000 chunk 331 optimal weight: 6.9990 chunk 133 optimal weight: 0.5980 chunk 164 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 457 optimal weight: 9.9990 chunk 411 optimal weight: 2.9990 chunk 271 optimal weight: 8.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 369 GLN G 392 ASN H 414 ASN ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.221907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.187444 restraints weight = 42751.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.181510 restraints weight = 70303.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.181704 restraints weight = 68953.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.182221 restraints weight = 52757.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.182650 restraints weight = 37570.143| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| r_final: 0.3900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 37712 Z= 0.137 Angle : 0.618 11.936 50863 Z= 0.300 Chirality : 0.044 0.250 6040 Planarity : 0.004 0.058 6444 Dihedral : 7.619 171.146 5263 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.72 % Rotamer: Outliers : 5.34 % Allowed : 28.19 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.12), residues: 4693 helix: 1.08 (0.11), residues: 2147 sheet: -1.47 (0.19), residues: 684 loop : -1.47 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 416 TYR 0.017 0.001 TYR B 192 PHE 0.010 0.001 PHE D 257 TRP 0.037 0.004 TRP E 283 HIS 0.007 0.001 HIS H 316 Details of bonding type rmsd covalent geometry : bond 0.00318 (37712) covalent geometry : angle 0.61820 (50863) hydrogen bonds : bond 0.03406 ( 1808) hydrogen bonds : angle 4.37802 ( 5175) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 352 time to evaluate : 1.085 Fit side-chains TARDY: cannot create tardy model for: "ASP A 449 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 449 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 139 THR cc_start: 0.1857 (OUTLIER) cc_final: 0.1428 (m) REVERT: A 209 TYR cc_start: 0.3902 (OUTLIER) cc_final: 0.3601 (m-80) REVERT: A 233 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5176 (mt-10) REVERT: A 281 LYS cc_start: 0.6992 (mmtt) cc_final: 0.6626 (mtmt) REVERT: A 317 ARG cc_start: 0.6922 (ttm170) cc_final: 0.6660 (mtt180) REVERT: A 396 GLU cc_start: 0.7189 (pt0) cc_final: 0.6878 (mt-10) REVERT: B 107 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.7006 (ptmm) REVERT: B 279 ILE cc_start: 0.7698 (mm) cc_final: 0.7424 (mm) REVERT: B 285 LYS cc_start: 0.6068 (OUTLIER) cc_final: 0.5864 (ttpp) REVERT: B 315 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7931 (mp) REVERT: B 408 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7334 (pt0) REVERT: B 451 GLN cc_start: 0.3662 (OUTLIER) cc_final: 0.3350 (mt0) REVERT: C 115 ASN cc_start: 0.8868 (m-40) cc_final: 0.8393 (m-40) REVERT: C 306 MET cc_start: 0.8128 (tpp) cc_final: 0.7901 (mmm) REVERT: C 342 GLU cc_start: 0.5833 (OUTLIER) cc_final: 0.5584 (pt0) REVERT: C 423 ASP cc_start: 0.5880 (p0) cc_final: 0.5129 (p0) REVERT: D 29 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.5687 (mtt-85) REVERT: D 65 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6165 (mp0) REVERT: D 282 GLU cc_start: 0.5255 (OUTLIER) cc_final: 0.5039 (mt-10) REVERT: D 416 ARG cc_start: 0.5210 (ppt170) cc_final: 0.4756 (tmm-80) REVERT: D 441 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6684 (tt0) REVERT: D 442 TYR cc_start: 0.6252 (m-80) cc_final: 0.6020 (m-10) REVERT: E 168 MET cc_start: 0.2851 (tmm) cc_final: 0.1935 (ttt) REVERT: E 179 ILE cc_start: 0.1065 (OUTLIER) cc_final: 0.0690 (pt) REVERT: E 356 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8264 (mt) REVERT: F 90 MET cc_start: 0.7849 (mtp) cc_final: 0.7581 (mtp) REVERT: F 113 MET cc_start: 0.7363 (mtm) cc_final: 0.7146 (mtt) REVERT: F 168 MET cc_start: 0.0905 (ptt) cc_final: 0.0619 (pmm) REVERT: G 280 ASN cc_start: 0.4466 (OUTLIER) cc_final: 0.4220 (m-40) REVERT: G 391 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6201 (mt) REVERT: H 39 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5386 (mt) REVERT: H 86 GLU cc_start: 0.5733 (mt-10) cc_final: 0.5470 (tp30) REVERT: H 91 VAL cc_start: 0.6072 (OUTLIER) cc_final: 0.5830 (m) REVERT: H 113 MET cc_start: 0.6462 (mtp) cc_final: 0.6064 (mtm) REVERT: H 114 GLU cc_start: 0.7534 (tt0) cc_final: 0.7146 (tt0) REVERT: H 170 LEU cc_start: 0.1282 (OUTLIER) cc_final: 0.0989 (pt) REVERT: H 238 VAL cc_start: 0.6704 (m) cc_final: 0.6338 (p) REVERT: H 352 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7027 (mm) REVERT: H 391 LEU cc_start: 0.5511 (mt) cc_final: 0.4967 (tp) REVERT: H 418 LYS cc_start: 0.6977 (mmpt) cc_final: 0.6236 (mtmt) REVERT: I 13 GLN cc_start: 0.5544 (pm20) cc_final: 0.5152 (pt0) REVERT: I 216 GLU cc_start: 0.0512 (OUTLIER) cc_final: 0.0130 (mm-30) REVERT: I 360 ILE cc_start: 0.8110 (tt) cc_final: 0.7814 (mt) REVERT: I 364 MET cc_start: 0.7599 (mmm) cc_final: 0.7370 (mmm) REVERT: I 384 ILE cc_start: 0.5499 (OUTLIER) cc_final: 0.5272 (mp) REVERT: I 388 GLU cc_start: 0.4279 (mm-30) cc_final: 0.2884 (tm-30) REVERT: J 168 MET cc_start: 0.4453 (mtt) cc_final: 0.2592 (ptp) REVERT: J 177 LYS cc_start: 0.1027 (OUTLIER) cc_final: 0.0769 (mttm) REVERT: J 179 ILE cc_start: 0.1635 (OUTLIER) cc_final: 0.1084 (tp) REVERT: J 241 THR cc_start: 0.3343 (OUTLIER) cc_final: 0.3023 (t) REVERT: J 310 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8078 (m) REVERT: J 415 LYS cc_start: 0.4888 (OUTLIER) cc_final: 0.3817 (tppt) REVERT: J 436 GLU cc_start: 0.5039 (OUTLIER) cc_final: 0.4672 (pt0) REVERT: J 441 GLN cc_start: 0.6730 (tm-30) cc_final: 0.6182 (pt0) REVERT: K 50 LEU cc_start: 0.5856 (OUTLIER) cc_final: 0.5508 (mt) REVERT: K 168 MET cc_start: 0.1191 (OUTLIER) cc_final: -0.0652 (mtp) REVERT: K 382 MET cc_start: 0.5523 (ptp) cc_final: 0.4989 (ptp) REVERT: K 388 THR cc_start: 0.6778 (p) cc_final: 0.6353 (t) REVERT: L 71 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6559 (mtt180) REVERT: L 112 GLU cc_start: 0.6107 (mp0) cc_final: 0.5585 (pt0) REVERT: L 143 VAL cc_start: 0.2056 (OUTLIER) cc_final: 0.1809 (p) REVERT: L 168 MET cc_start: 0.2601 (mmt) cc_final: 0.2149 (mtt) REVERT: L 203 SER cc_start: 0.4242 (OUTLIER) cc_final: 0.3599 (p) REVERT: L 303 MET cc_start: 0.7654 (tpp) cc_final: 0.7325 (mmm) REVERT: L 358 SER cc_start: 0.7699 (p) cc_final: 0.7273 (t) REVERT: L 414 ARG cc_start: 0.6410 (mtm110) cc_final: 0.5994 (mpt180) outliers start: 216 outliers final: 171 residues processed: 548 average time/residue: 0.2119 time to fit residues: 193.2202 Evaluate side-chains 541 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 337 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 388 THR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 442 TYR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 164 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain G residue 435 GLU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 352 LEU Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 335 ASN Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 367 THR Chi-restraints excluded: chain I residue 380 GLN Chi-restraints excluded: chain I residue 384 ILE Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain I residue 433 ILE Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 310 SER Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 332 ILE Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 358 SER Chi-restraints excluded: chain J residue 415 LYS Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain J residue 436 GLU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 168 MET Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 203 SER Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 346 ILE Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 357 VAL Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain K residue 431 SER Chi-restraints excluded: chain K residue 437 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 437 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 372 optimal weight: 4.9990 chunk 202 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 387 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 385 optimal weight: 0.0020 chunk 208 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN D 25 HIS G 392 ASN H 451 GLN L 233 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.216666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.205299 restraints weight = 42797.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.201468 restraints weight = 87865.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.193840 restraints weight = 100960.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.190006 restraints weight = 85305.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.186459 restraints weight = 82017.648| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| r_final: 0.3985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 37712 Z= 0.209 Angle : 0.711 12.008 50863 Z= 0.348 Chirality : 0.047 0.298 6040 Planarity : 0.005 0.061 6444 Dihedral : 7.882 169.145 5263 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.58 % Favored : 94.23 % Rotamer: Outliers : 5.68 % Allowed : 27.92 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.12), residues: 4693 helix: 0.79 (0.11), residues: 2141 sheet: -1.54 (0.19), residues: 696 loop : -1.61 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 416 TYR 0.018 0.002 TYR B 192 PHE 0.012 0.002 PHE K 123 TRP 0.054 0.005 TRP E 283 HIS 0.009 0.002 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00506 (37712) covalent geometry : angle 0.71118 (50863) hydrogen bonds : bond 0.04134 ( 1808) hydrogen bonds : angle 4.62400 ( 5175) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6960.86 seconds wall clock time: 121 minutes 9.83 seconds (7269.83 seconds total)