Starting phenix.real_space_refine on Mon Aug 10 07:27:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gfb_51312/08_2026/9gfb_51312.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gfb_51312/08_2026/9gfb_51312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gfb_51312/08_2026/9gfb_51312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gfb_51312/08_2026/9gfb_51312.map" model { file = "/net/cci-nas-00/data/ceres_data/9gfb_51312/08_2026/9gfb_51312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gfb_51312/08_2026/9gfb_51312.cif" } resolution = 3.55 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= 0.003 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 293 5.49 5 S 170 5.16 5 C 26247 2.51 5 N 7721 2.21 5 O 8700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 344 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43132 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3344 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 16, 'TRANS': 417} Chain breaks: 1 Chain: "B" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3453 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 16, 'TRANS': 430} Chain breaks: 1 Chain: "C" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3412 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 17, 'TRANS': 425} Chain: "D" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3317 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 10, 'TRANS': 415} Chain breaks: 2 Chain: "E" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3403 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 11, 'TRANS': 427} Chain: "F" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3376 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 11, 'TRANS': 422} Chain breaks: 1 Chain: "G" Number of atoms: 5608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5608 Classifications: {'peptide': 682} Link IDs: {'PTRANS': 28, 'TRANS': 653} Chain breaks: 3 Chain: "H" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1188 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 13, 'TRANS': 137} Chain breaks: 2 Chain: "I" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 842 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "J" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3277 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 29, 'TRANS': 382} Chain breaks: 2 Chain: "K" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2868 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "L" Number of atoms: 2831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2831 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "M" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 756 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "N" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "O" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "P" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Q" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "R" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "S" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "T" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.65, per 1000 atoms: 0.22 Number of scatterers: 43132 At special positions: 0 Unit cell: (134.272, 189.869, 208.751, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 170 16.00 P 293 15.00 O 8700 8.00 N 7721 7.00 C 26247 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: 3.99 Conformation dependent library (CDL) restraints added in 1.8 seconds 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8800 Finding SS restraints... Secondary structure from input PDB file: 209 helices and 39 sheets defined 50.2% alpha, 10.2% beta 136 base pairs and 229 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.649A pdb=" N ALA A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 99 through 102 removed outlier: 3.881A pdb=" N TYR A 102 " --> pdb=" O SER A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 107 through 119 removed outlier: 4.098A pdb=" N MET A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 183 removed outlier: 3.831A pdb=" N SER A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) 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 240 through 249 removed outlier: 4.172A pdb=" N ARG A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.639A pdb=" N LEU A 263 " --> pdb=" O MET A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 289 removed outlier: 4.251A pdb=" N GLU A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 308 through 319 removed outlier: 4.443A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 367 through 383 removed outlier: 4.146A pdb=" N GLN A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 402 through 420 removed outlier: 4.039A pdb=" N LEU A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.648A pdb=" N VAL A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 450 removed outlier: 3.550A pdb=" N LYS A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 454 removed outlier: 3.541A pdb=" N TYR A 454 " --> pdb=" O GLN A 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'B' and resid 42 through 59 removed outlier: 3.508A pdb=" N GLU B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 removed outlier: 3.539A pdb=" N GLY B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 removed outlier: 3.734A 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 removed outlier: 4.755A pdb=" N MET B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 removed outlier: 3.641A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 272 through 289 removed outlier: 3.530A pdb=" N ARG B 276 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 308 through 319 removed outlier: 4.150A pdb=" N ARG B 317 " --> pdb=" O THR B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 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 420 Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.586A pdb=" N VAL B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 450 removed outlier: 3.553A pdb=" N LYS B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 454 removed outlier: 4.133A pdb=" N TYR B 454 " --> pdb=" O GLN B 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 451 through 454' Processing helix chain 'C' and resid 42 through 58 Processing helix chain 'C' and resid 75 through 88 removed outlier: 3.707A pdb=" N ALA C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 175 through 183 removed outlier: 4.319A pdb=" N SER C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 210 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 272 through 289 removed outlier: 3.538A pdb=" N ARG C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 321 removed outlier: 4.581A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (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 removed outlier: 3.539A pdb=" N GLN C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 409 through 420 Processing helix chain 'C' and resid 426 through 437 removed outlier: 3.641A pdb=" N VAL C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 449 removed outlier: 3.656A pdb=" N LYS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 454 removed outlier: 3.894A pdb=" N TYR C 454 " --> pdb=" O GLN C 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.854A pdb=" N ARG D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.666A pdb=" N ALA D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.720A pdb=" N PHE D 109 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 114 through 125 removed outlier: 3.509A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 183 removed outlier: 3.990A pdb=" N SER D 181 " --> pdb=" O LYS D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.596A pdb=" N ILE D 250 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN D 251 " --> pdb=" O ILE D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.593A pdb=" N LEU D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 286 removed outlier: 3.528A pdb=" N ARG D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.766A pdb=" N MET D 303 " --> pdb=" O GLU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.901A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 347 through 352 Processing helix chain 'D' and resid 363 through 379 Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 399 through 417 removed outlier: 3.958A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 435 through 445 removed outlier: 3.573A pdb=" N GLU D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 66 Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 106 through 109 Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 175 through 185 removed outlier: 4.682A pdb=" N SER E 181 " --> pdb=" O LYS E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 269 through 286 removed outlier: 3.588A pdb=" N ARG E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 305 through 316 removed outlier: 4.171A pdb=" N ARG E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 346 Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 363 through 378 removed outlier: 4.118A pdb=" N GLN E 369 " --> pdb=" O LYS E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 398 through 416 removed outlier: 4.133A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 433 Processing helix chain 'E' and resid 435 through 446 removed outlier: 3.712A pdb=" N LYS E 444 " --> pdb=" O THR E 440 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU E 445 " --> pdb=" O GLN E 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 removed outlier: 4.073A pdb=" N GLN F 92 " --> pdb=" O MET F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 109 removed outlier: 3.814A pdb=" N PHE F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 109' Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 175 through 186 removed outlier: 3.760A pdb=" N GLU F 180 " --> pdb=" O THR F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 244 through 251 removed outlier: 3.692A pdb=" N ASN F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 257 No H-bonds generated for 'chain 'F' and resid 255 through 257' Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 269 through 287 removed outlier: 3.619A pdb=" N ARG F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.623A pdb=" N PHE F 311 " --> pdb=" O GLU F 307 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 346 Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 379 Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.581A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 435 through 445 Processing helix chain 'F' and resid 446 through 450 Processing helix chain 'G' and resid 519 through 536 removed outlier: 3.906A pdb=" N ASN G 531 " --> pdb=" O ASN G 527 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU G 532 " --> pdb=" O TRP G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 548 through 559 removed outlier: 4.979A pdb=" N LEU G 557 " --> pdb=" O SER G 553 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA G 558 " --> pdb=" O ILE G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 563 through 568 Processing helix chain 'G' and resid 575 through 577 No H-bonds generated for 'chain 'G' and resid 575 through 577' Processing helix chain 'G' and resid 578 through 590 removed outlier: 3.721A pdb=" N THR G 587 " --> pdb=" O HIS G 583 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL G 590 " --> pdb=" O PHE G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 610 Processing helix chain 'G' and resid 611 through 613 No H-bonds generated for 'chain 'G' and resid 611 through 613' Processing helix chain 'G' and resid 631 through 637 Processing helix chain 'G' and resid 637 through 642 Processing helix chain 'G' and resid 654 through 658 Processing helix chain 'G' and resid 662 through 669 Processing helix chain 'G' and resid 687 through 699 removed outlier: 3.662A pdb=" N LEU G 691 " --> pdb=" O THR G 687 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU G 694 " --> pdb=" O GLU G 690 " (cutoff:3.500A) Processing helix chain 'G' and resid 705 through 712 Processing helix chain 'G' and resid 730 through 740 Processing helix chain 'G' and resid 747 through 751 Processing helix chain 'G' and resid 768 through 780 Processing helix chain 'G' and resid 809 through 818 Processing helix chain 'G' and resid 819 through 822 Processing helix chain 'G' and resid 841 through 848 Processing helix chain 'G' and resid 849 through 854 Processing helix chain 'G' and resid 854 through 864 removed outlier: 3.877A pdb=" N TRP G 860 " --> pdb=" O SER G 856 " (cutoff:3.500A) Processing helix chain 'G' and resid 868 through 877 Processing helix chain 'G' and resid 888 through 893 Processing helix chain 'G' and resid 897 through 907 Processing helix chain 'G' and resid 908 through 933 removed outlier: 3.923A pdb=" N TYR G 924 " --> pdb=" O LEU G 920 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG G 925 " --> pdb=" O LYS G 921 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU G 929 " --> pdb=" O ARG G 925 " (cutoff:3.500A) Processing helix chain 'G' and resid 958 through 965 Processing helix chain 'G' and resid 965 through 972 removed outlier: 3.554A pdb=" N SER G 970 " --> pdb=" O PRO G 966 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU G 971 " --> pdb=" O LEU G 967 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL G 972 " --> pdb=" O LEU G 968 " (cutoff:3.500A) Processing helix chain 'G' and resid 1028 through 1040 Processing helix chain 'G' and resid 1043 through 1053 Processing helix chain 'G' and resid 1054 through 1065 removed outlier: 4.178A pdb=" N ASN G1063 " --> pdb=" O ALA G1059 " (cutoff:3.500A) Processing helix chain 'G' and resid 1075 through 1079 Processing helix chain 'G' and resid 1094 through 1099 Processing helix chain 'G' and resid 1100 through 1117 Processing helix chain 'G' and resid 1126 through 1140 Processing helix chain 'G' and resid 1152 through 1164 removed outlier: 4.081A pdb=" N VAL G1160 " --> pdb=" O ARG G1156 " (cutoff:3.500A) Processing helix chain 'G' and resid 1201 through 1209 Processing helix chain 'G' and resid 1230 through 1248 removed outlier: 4.457A pdb=" N ARG G1246 " --> pdb=" O SER G1242 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET G1247 " --> pdb=" O GLU G1243 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL G1248 " --> pdb=" O ILE G1244 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 159 removed outlier: 6.075A pdb=" N GLU H 148 " --> pdb=" O GLN H 144 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 176 removed outlier: 3.511A pdb=" N LEU H 175 " --> pdb=" O ASN H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 188 Processing helix chain 'H' and resid 209 through 235 removed outlier: 3.950A pdb=" N LYS H 215 " --> pdb=" O GLU H 211 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG H 224 " --> pdb=" O ALA H 220 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA H 227 " --> pdb=" O ARG H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 340 Processing helix chain 'I' and resid 143 through 152 Processing helix chain 'I' and resid 199 through 207 Processing helix chain 'I' and resid 210 through 220 Processing helix chain 'J' and resid 106 through 121 removed outlier: 4.302A pdb=" N LEU J 112 " --> pdb=" O LEU J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 157 removed outlier: 4.539A pdb=" N CYS J 155 " --> pdb=" O LEU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 175 Processing helix chain 'J' and resid 214 through 230 Processing helix chain 'J' and resid 231 through 234 removed outlier: 3.843A pdb=" N LEU J 234 " --> pdb=" O PRO J 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 231 through 234' Processing helix chain 'J' and resid 238 through 248 removed outlier: 4.286A pdb=" N GLU J 244 " --> pdb=" O SER J 240 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE J 245 " --> pdb=" O ARG J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 264 Processing helix chain 'J' and resid 265 through 273 Processing helix chain 'J' and resid 446 through 454 removed outlier: 3.535A pdb=" N ALA J 451 " --> pdb=" O GLU J 447 " (cutoff:3.500A) Proline residue: J 452 - end of helix Processing helix chain 'J' and resid 455 through 456 No H-bonds generated for 'chain 'J' and resid 455 through 456' Processing helix chain 'J' and resid 457 through 461 Processing helix chain 'J' and resid 466 through 475 removed outlier: 3.771A pdb=" N LEU J 472 " --> pdb=" O ILE J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 480 through 489 removed outlier: 4.307A pdb=" N GLU J 485 " --> pdb=" O LYS J 481 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET J 486 " --> pdb=" O ASP J 482 " (cutoff:3.500A) Processing helix chain 'J' and resid 497 through 500 Processing helix chain 'J' and resid 502 through 515 removed outlier: 4.209A pdb=" N GLU J 513 " --> pdb=" O LYS J 509 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET J 514 " --> pdb=" O GLU J 510 " (cutoff:3.500A) Processing helix chain 'J' and resid 531 through 544 Processing helix chain 'J' and resid 555 through 560 removed outlier: 3.949A pdb=" N GLU J 559 " --> pdb=" O LYS J 555 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 57 removed outlier: 4.044A pdb=" N LEU M 48 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG M 49 " --> pdb=" O THR M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.750A pdb=" N VAL M 89 " --> pdb=" O GLN M 85 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 132 removed outlier: 3.510A pdb=" N ILE M 124 " --> pdb=" O MET M 120 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG M 129 " --> pdb=" O GLN M 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 29 Processing helix chain 'N' and resid 30 through 41 Processing helix chain 'N' and resid 49 through 76 removed outlier: 4.210A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA N 76 " --> pdb=" O TYR N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 93 removed outlier: 3.648A pdb=" N VAL N 86 " --> pdb=" O THR N 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 22 removed outlier: 3.644A pdb=" N ARG O 20 " --> pdb=" O THR O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 45 through 73 removed outlier: 4.190A pdb=" N VAL O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU O 65 " --> pdb=" O GLU O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 90 removed outlier: 3.792A pdb=" N ASP O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 97 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'P' and resid 37 through 47 Processing helix chain 'P' and resid 55 through 84 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.110A pdb=" N THR P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG P 99 " --> pdb=" O GLN P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 123 removed outlier: 3.973A pdb=" N LYS P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 55 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 3.656A pdb=" N PHE Q 67 " --> pdb=" O ARG Q 63 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG Q 72 " --> pdb=" O GLN Q 68 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 removed outlier: 4.006A pdb=" N MET Q 90 " --> pdb=" O SER Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 131 removed outlier: 4.078A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 Processing helix chain 'R' and resid 30 through 41 Processing helix chain 'R' and resid 49 through 76 removed outlier: 4.362A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP R 68 " --> pdb=" O ASN R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing helix chain 'S' and resid 16 through 22 Processing helix chain 'S' and resid 26 through 37 Processing helix chain 'S' and resid 46 through 73 Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.620A pdb=" N LEU S 83 " --> pdb=" O ILE S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 97 Processing helix chain 'T' and resid 37 through 49 Processing helix chain 'T' and resid 55 through 84 Processing helix chain 'T' and resid 90 through 102 Processing helix chain 'T' and resid 104 through 122 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: 6.376A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 140 removed outlier: 5.609A pdb=" N VAL A 135 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS A 162 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU A 137 " --> pdb=" O GLY A 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 172 current: chain 'A' and resid 200 through 206 removed outlier: 5.264A pdb=" N VAL A 221 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ARG A 205 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 6 removed outlier: 6.709A pdb=" N ILE B 3 " --> pdb=" O LEU G 762 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N TYR G 764 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU B 5 " --> pdb=" O TYR G 764 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU G1121 " --> pdb=" O ILE G1192 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N MET G1145 " --> pdb=" O LEU G1173 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N SER G1175 " --> pdb=" O MET G1145 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU G1147 " --> pdb=" O SER G1175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 97 removed outlier: 6.343A pdb=" N LEU B 299 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ALA B 330 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL B 301 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL B 66 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N SER B 331 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 68 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 143 removed outlier: 5.745A pdb=" N VAL B 135 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS B 162 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS B 156 " --> pdb=" O CYS B 141 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N THR B 143 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE B 154 " --> pdb=" O THR B 143 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 166 through 172 current: chain 'B' and resid 199 through 206 removed outlier: 6.117A pdb=" N VAL B 221 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ARG B 205 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.916A pdb=" N ALA C 65 " --> pdb=" O MET C 359 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE C 361 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU C 67 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 120 through 142 removed outlier: 5.695A pdb=" N VAL C 135 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS C 162 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU C 137 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS C 156 " --> pdb=" O CYS C 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 167 through 172 current: chain 'C' and resid 200 through 205 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 200 through 205 current: chain 'E' and resid 158 through 164 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 173 current: chain 'E' and resid 204 through 207 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 204 through 207 current: chain 'G' and resid 996 through 1005 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 996 through 1005 current: chain 'H' and resid 283 through 286 Processing sheet with id=AB2, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB3, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.521A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU D 296 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA D 327 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE D 298 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 147 removed outlier: 6.896A pdb=" N THR D 162 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE D 145 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS D 160 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY D 159 " --> pdb=" O LEU D 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 169 through 174 current: chain 'D' and resid 202 through 208 removed outlier: 6.290A pdb=" N VAL D 225 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ARG D 207 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AB6, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB7, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.461A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU E 296 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ALA E 327 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE E 298 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 333 through 334 Processing sheet with id=AB9, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC1, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.511A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR F 328 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 127 through 147 removed outlier: 5.358A pdb=" N VAL F 142 " --> pdb=" O LYS F 164 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS F 164 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU F 144 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY F 159 " --> pdb=" O LEU F 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 168 through 174 current: chain 'F' and resid 202 through 208 removed outlier: 5.906A pdb=" N VAL F 225 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ARG F 207 " --> pdb=" O VAL F 225 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 224 through 225 current: chain 'H' and resid 328 through 329 Processing sheet with id=AC3, first strand: chain 'F' and resid 333 through 334 Processing sheet with id=AC4, first strand: chain 'G' and resid 595 through 597 removed outlier: 7.100A pdb=" N LEU G 596 " --> pdb=" O ILE G 628 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N SER G 630 " --> pdb=" O LEU G 596 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU G 571 " --> pdb=" O VAL G 650 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASP G 652 " --> pdb=" O LEU G 571 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE G 573 " --> pdb=" O ASP G 652 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N MET G 649 " --> pdb=" O LEU G 677 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N LEU G 679 " --> pdb=" O MET G 649 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU G 651 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY G 539 " --> pdb=" O ARG G 676 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE G 540 " --> pdb=" O LEU G 744 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 831 through 833 removed outlier: 6.011A pdb=" N PHE G 831 " --> pdb=" O THR G1018 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'G' and resid 838 through 840 Processing sheet with id=AC7, first strand: chain 'I' and resid 188 through 189 Processing sheet with id=AC8, first strand: chain 'J' and resid 43 through 46 removed outlier: 3.671A pdb=" N ARG J 43 " --> pdb=" O ASP J 36 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU J 33 " --> pdb=" O VAL J 133 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N THR J 135 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU J 35 " --> pdb=" O THR J 135 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 66 through 67 Processing sheet with id=AD1, first strand: chain 'J' and resid 98 through 99 Processing sheet with id=AD2, first strand: chain 'J' and resid 183 through 188 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 202 through 203 current: chain 'J' and resid 523 through 525 Processing sheet with id=AD3, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.803A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AD5, first strand: chain 'N' and resid 96 through 98 Processing sheet with id=AD6, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.144A pdb=" N ARG O 42 " --> pdb=" O ILE P 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AD8, first strand: chain 'O' and resid 100 through 102 removed outlier: 6.728A pdb=" N THR O 101 " --> pdb=" O TYR R 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'Q' and resid 83 through 84 removed outlier: 6.992A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'Q' and resid 118 through 119 Processing sheet with id=AE2, first strand: chain 'S' and resid 42 through 43 removed outlier: 7.047A pdb=" N ARG S 42 " --> pdb=" O ILE T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'S' and resid 77 through 78 1609 hydrogen bonds defined for protein. 4620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 696 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 229 stacking parallelities Total time for adding SS restraints: 13.30 Time building geometry restraints manager: 5.29 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: 10679 1.33 - 1.45: 9152 1.45 - 1.58: 23751 1.58 - 1.70: 561 1.70 - 1.82: 281 Bond restraints: 44424 Sorted by residual: bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.341 0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.341 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.341 0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" C4 ADP D 501 " pdb=" C5 ADP D 501 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.44e+01 ... (remaining 44419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 58763 3.94 - 7.87: 2340 7.87 - 11.81: 41 11.81 - 15.75: 9 15.75 - 19.68: 5 Bond angle restraints: 61158 Sorted by residual: angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 117.15 19.68 1.00e+00 1.00e+00 3.87e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 120.25 19.62 1.00e+00 1.00e+00 3.85e+02 angle pdb=" O5' DG L -33 " pdb=" C5' DG L -33 " pdb=" C4' DG L -33 " ideal model delta sigma weight residual 109.40 118.17 -8.77 8.00e-01 1.56e+00 1.20e+02 angle pdb=" O4' DG K -47 " pdb=" C1' DG K -47 " pdb=" N9 DG K -47 " ideal model delta sigma weight residual 108.00 115.15 -7.15 7.00e-01 2.04e+00 1.04e+02 angle pdb=" N6 DA K 48 " pdb=" C6 DA K 48 " pdb=" N1 DA K 48 " ideal model delta sigma weight residual 118.60 112.49 6.11 6.00e-01 2.78e+00 1.04e+02 ... (remaining 61153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.15: 24677 32.15 - 64.30: 1633 64.30 - 96.44: 113 96.44 - 128.59: 6 128.59 - 160.74: 3 Dihedral angle restraints: 26432 sinusoidal: 12787 harmonic: 13645 Sorted by residual: dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual 300.00 162.94 137.07 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" C5' ADP F 501 " pdb=" O5' ADP F 501 " pdb=" PA ADP F 501 " pdb=" O2A ADP F 501 " ideal model delta sinusoidal sigma weight residual 300.00 170.77 129.23 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" O1B ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PB ADP C 501 " pdb=" PA ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 65.60 -125.60 1 2.00e+01 2.50e-03 3.80e+01 ... (remaining 26429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 5148 0.104 - 0.208: 1597 0.208 - 0.311: 168 0.311 - 0.415: 23 0.415 - 0.519: 6 Chirality restraints: 6942 Sorted by residual: chirality pdb=" C3' DC L 20 " pdb=" C4' DC L 20 " pdb=" O3' DC L 20 " pdb=" C2' DC L 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.21 -0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" CA ASN B 420 " pdb=" N ASN B 420 " pdb=" C ASN B 420 " pdb=" CB ASN B 420 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CA LYS I 222 " pdb=" N LYS I 222 " pdb=" C LYS I 222 " pdb=" CB LYS I 222 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.77e+00 ... (remaining 6939 not shown) Planarity restraints: 6851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT K -24 " -0.202 2.00e-02 2.50e+03 1.40e-01 4.89e+02 pdb=" N1 DT K -24 " -0.076 2.00e-02 2.50e+03 pdb=" C2 DT K -24 " 0.025 2.00e-02 2.50e+03 pdb=" O2 DT K -24 " 0.261 2.00e-02 2.50e+03 pdb=" N3 DT K -24 " -0.028 2.00e-02 2.50e+03 pdb=" C4 DT K -24 " -0.045 2.00e-02 2.50e+03 pdb=" O4 DT K -24 " -0.199 2.00e-02 2.50e+03 pdb=" C5 DT K -24 " 0.057 2.00e-02 2.50e+03 pdb=" C7 DT K -24 " 0.183 2.00e-02 2.50e+03 pdb=" C6 DT K -24 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT L -21 " -0.248 2.00e-02 2.50e+03 1.37e-01 4.71e+02 pdb=" N1 DT L -21 " -0.013 2.00e-02 2.50e+03 pdb=" C2 DT L -21 " 0.040 2.00e-02 2.50e+03 pdb=" O2 DT L -21 " 0.235 2.00e-02 2.50e+03 pdb=" N3 DT L -21 " -0.030 2.00e-02 2.50e+03 pdb=" C4 DT L -21 " -0.055 2.00e-02 2.50e+03 pdb=" O4 DT L -21 " -0.192 2.00e-02 2.50e+03 pdb=" C5 DT L -21 " 0.053 2.00e-02 2.50e+03 pdb=" C7 DT L -21 " 0.151 2.00e-02 2.50e+03 pdb=" C6 DT L -21 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG K 26 " 0.280 2.00e-02 2.50e+03 1.18e-01 4.18e+02 pdb=" N9 DG K 26 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG K 26 " -0.148 2.00e-02 2.50e+03 pdb=" N7 DG K 26 " -0.118 2.00e-02 2.50e+03 pdb=" C5 DG K 26 " -0.037 2.00e-02 2.50e+03 pdb=" C6 DG K 26 " 0.063 2.00e-02 2.50e+03 pdb=" O6 DG K 26 " 0.165 2.00e-02 2.50e+03 pdb=" N1 DG K 26 " 0.055 2.00e-02 2.50e+03 pdb=" C2 DG K 26 " -0.018 2.00e-02 2.50e+03 pdb=" N2 DG K 26 " -0.098 2.00e-02 2.50e+03 pdb=" N3 DG K 26 " -0.059 2.00e-02 2.50e+03 pdb=" C4 DG K 26 " -0.059 2.00e-02 2.50e+03 ... (remaining 6848 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 4 2.39 - 3.02: 22444 3.02 - 3.65: 65965 3.65 - 4.27: 103589 4.27 - 4.90: 165887 Nonbonded interactions: 357889 Sorted by model distance: nonbonded pdb=" O VAL H 311 " pdb="ZN ZN H 401 " model vdw 1.764 2.230 nonbonded pdb=" O CYS H 309 " pdb="ZN ZN H 401 " model vdw 1.764 2.230 nonbonded pdb=" O SER H 310 " pdb="ZN ZN H 401 " model vdw 1.818 2.230 nonbonded pdb=" C SER H 310 " pdb="ZN ZN H 401 " model vdw 2.359 2.460 nonbonded pdb=" OG SER G1175 " pdb=" OP1 DT L -69 " model vdw 2.501 3.040 ... (remaining 357884 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 12 through 141 or resid 152 through 454)) selection = (chain 'B' and (resid 12 through 141 or resid 152 through 454)) selection = (chain 'C' and (resid 12 through 141 or resid 152 through 454)) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 15 through 149 or resid 156 through 214 or resid 222 throu \ gh 501)) selection = (chain 'F' and (resid 15 through 149 or resid 156 through 214 or resid 222 throu \ gh 501)) } ncs_group { reference = chain 'M' selection = (chain 'Q' and resid 43 through 135) } ncs_group { reference = (chain 'N' and resid 24 through 102) selection = chain 'R' } ncs_group { reference = chain 'O' selection = (chain 'S' and resid 13 through 118) } ncs_group { reference = (chain 'P' and resid 31 through 123) selection = chain 'T' } 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=0.01 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: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.880 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 48.280 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.110 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.013 0.149 44424 Z= 0.924 Angle : 1.872 19.684 61158 Z= 1.470 Chirality : 0.094 0.519 6942 Planarity : 0.021 0.253 6851 Dihedral : 19.026 160.741 17632 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.15 % Favored : 95.21 % Rotamer: Outliers : 0.87 % Allowed : 5.36 % Favored : 93.77 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.95 (0.11), residues: 4675 helix: -1.59 (0.09), residues: 2172 sheet: -0.29 (0.21), residues: 538 loop : -1.02 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG G1209 TYR 0.152 0.023 TYR S 57 PHE 0.080 0.014 PHE J 98 TRP 0.122 0.023 TRP J 263 HIS 0.019 0.004 HIS F 302 Details of bonding type rmsd/Z covalent geometry : bond 0.01252 / 0.92 (44424) covalent geometry : angle 1.87189 / 1.47 (61158) hydrogen bonds : bond 0.15708 / 10.38 ( 1957) hydrogen bonds : angle 7.40651 / 5.11 ( 5316) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 911 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ARG cc_start: 0.7462 (mtt-85) cc_final: 0.7162 (ttm-80) REVERT: A 299 LEU cc_start: 0.9177 (tp) cc_final: 0.8916 (tp) REVERT: A 415 LEU cc_start: 0.9288 (tp) cc_final: 0.9061 (mt) REVERT: B 113 MET cc_start: 0.8748 (mmm) cc_final: 0.8495 (tpt) REVERT: C 113 MET cc_start: 0.8430 (tpt) cc_final: 0.8177 (tpt) REVERT: C 134 GLU cc_start: 0.8468 (tt0) cc_final: 0.7767 (tm-30) REVERT: C 192 TYR cc_start: 0.9157 (p90) cc_final: 0.8675 (p90) REVERT: C 259 MET cc_start: 0.8577 (mtp) cc_final: 0.8355 (mmm) REVERT: C 278 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8090 (mm-30) REVERT: D 111 LEU cc_start: 0.8999 (tp) cc_final: 0.8786 (tp) REVERT: D 313 ASN cc_start: 0.8155 (m110) cc_final: 0.7551 (t0) REVERT: D 349 ASP cc_start: 0.6022 (t0) cc_final: 0.5636 (t0) REVERT: E 26 SER cc_start: 0.8575 (m) cc_final: 0.8361 (p) REVERT: E 313 ASN cc_start: 0.8658 (m-40) cc_final: 0.7944 (m-40) REVERT: F 132 LYS cc_start: 0.8672 (mttp) cc_final: 0.8430 (mmmm) REVERT: F 288 LYS cc_start: 0.8537 (mttt) cc_final: 0.8328 (mtpt) REVERT: F 291 ILE cc_start: 0.9322 (mt) cc_final: 0.9069 (tt) REVERT: G 628 ILE cc_start: 0.8589 (mm) cc_final: 0.8040 (mm) REVERT: G 709 PHE cc_start: 0.7949 (t80) cc_final: 0.7689 (t80) REVERT: G 901 MET cc_start: 0.9084 (tpt) cc_final: 0.8430 (tpt) REVERT: G 929 LEU cc_start: 0.9033 (tt) cc_final: 0.8623 (mt) REVERT: G 1184 ASN cc_start: 0.5514 (m-40) cc_final: 0.4958 (p0) REVERT: H 215 LYS cc_start: 0.5667 (tttp) cc_final: 0.5276 (mmtt) REVERT: H 337 ILE cc_start: 0.8959 (mm) cc_final: 0.8094 (mm) REVERT: I 148 LEU cc_start: 0.8633 (mm) cc_final: 0.8146 (mm) REVERT: I 181 VAL cc_start: 0.9287 (m) cc_final: 0.8840 (p) REVERT: I 213 VAL cc_start: 0.8994 (m) cc_final: 0.8748 (p) REVERT: J 48 CYS cc_start: 0.8561 (t) cc_final: 0.8198 (p) REVERT: J 114 ASP cc_start: 0.8338 (m-30) cc_final: 0.7289 (m-30) REVERT: J 163 TYR cc_start: 0.7264 (m-80) cc_final: 0.6972 (m-10) REVERT: J 213 LEU cc_start: 0.8836 (mp) cc_final: 0.8215 (mp) REVERT: J 276 MET cc_start: 0.6995 (mmm) cc_final: 0.6722 (mmm) REVERT: M 54 TYR cc_start: 0.8531 (m-80) cc_final: 0.8189 (m-10) REVERT: N 35 ARG cc_start: 0.9159 (mtt180) cc_final: 0.8906 (mmm160) REVERT: N 90 LEU cc_start: 0.9050 (mt) cc_final: 0.8834 (mp) REVERT: O 91 GLU cc_start: 0.8976 (pm20) cc_final: 0.8745 (pp20) REVERT: P 94 ILE cc_start: 0.8136 (mm) cc_final: 0.7829 (mm) REVERT: P 100 LEU cc_start: 0.8807 (mt) cc_final: 0.8584 (tp) REVERT: Q 76 GLN cc_start: 0.8473 (pp30) cc_final: 0.7912 (mm110) REVERT: Q 85 GLN cc_start: 0.8598 (mt0) cc_final: 0.7912 (mm-40) REVERT: Q 107 THR cc_start: 0.8860 (m) cc_final: 0.8614 (m) REVERT: Q 134 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7701 (ptt90) REVERT: S 68 ASN cc_start: 0.7958 (m-40) cc_final: 0.7719 (m110) REVERT: S 100 VAL cc_start: 0.7592 (p) cc_final: 0.6874 (p) REVERT: T 46 LYS cc_start: 0.8748 (mmtm) cc_final: 0.8548 (mtmm) REVERT: T 59 MET cc_start: 0.9027 (tpp) cc_final: 0.8681 (tpp) REVERT: T 70 PHE cc_start: 0.8466 (t80) cc_final: 0.8202 (t80) REVERT: T 95 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8321 (tp40) REVERT: T 96 THR cc_start: 0.8553 (m) cc_final: 0.8315 (p) REVERT: T 109 HIS cc_start: 0.8490 (m-70) cc_final: 0.7831 (m90) outliers start: 35 outliers final: 10 residues processed: 936 average time/residue: 0.2961 time to fit residues: 440.4886 Evaluate side-chains 568 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 557 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain T residue 95 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 348 HIS C 20 HIS C 408 GLN D 92 GLN D 146 GLN E 255 GLN ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN F 240 HIS ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 672 GLN G 989 HIS G1164 GLN ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 236 ASN ** I 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 ASN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 568 HIS M 93 GLN M 113 HIS N 25 ASN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 84 GLN P 67 ASN ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.113511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073544 restraints weight = 108811.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075695 restraints weight = 47725.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.077066 restraints weight = 27561.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.077963 restraints weight = 19132.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.078519 restraints weight = 15025.785| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 44424 Z= 0.194 Angle : 0.839 9.099 61158 Z= 0.449 Chirality : 0.053 0.317 6942 Planarity : 0.005 0.051 6851 Dihedral : 21.688 172.660 8327 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.91 % Favored : 96.96 % Rotamer: Outliers : 2.78 % Allowed : 11.17 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.99 (0.12), residues: 4675 helix: -0.41 (0.10), residues: 2207 sheet: -0.64 (0.20), residues: 609 loop : -0.74 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 86 TYR 0.022 0.003 TYR J 557 PHE 0.032 0.002 PHE M 67 TRP 0.027 0.002 TRP J 540 HIS 0.019 0.002 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (44424) covalent geometry : angle 0.83931 / 0.45 (61158) hydrogen bonds : bond 0.06025 / 3.94 ( 1957) hydrogen bonds : angle 4.97664 / 3.43 ( 5316) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 620 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 SER cc_start: 0.9292 (t) cc_final: 0.9043 (p) REVERT: B 113 MET cc_start: 0.8796 (mmm) cc_final: 0.8543 (tpp) REVERT: B 218 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6312 (mm-30) REVERT: C 102 TYR cc_start: 0.8439 (m-80) cc_final: 0.8199 (m-80) REVERT: C 244 ASP cc_start: 0.8336 (m-30) cc_final: 0.8104 (m-30) REVERT: C 408 GLN cc_start: 0.8722 (tt0) cc_final: 0.8489 (mt0) REVERT: D 35 ASP cc_start: 0.8434 (m-30) cc_final: 0.8113 (t70) REVERT: D 46 MET cc_start: 0.8377 (ptm) cc_final: 0.8134 (ttt) REVERT: E 178 MET cc_start: 0.8645 (tmm) cc_final: 0.7921 (tmm) REVERT: E 201 LYS cc_start: 0.9126 (mttp) cc_final: 0.8896 (mtmm) REVERT: E 264 ASP cc_start: 0.7944 (t0) cc_final: 0.6963 (t0) REVERT: F 46 MET cc_start: 0.8093 (mtp) cc_final: 0.7797 (mtp) REVERT: F 144 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: F 291 ILE cc_start: 0.9234 (mt) cc_final: 0.9015 (tt) REVERT: G 929 LEU cc_start: 0.9109 (tt) cc_final: 0.8850 (mt) REVERT: G 1048 GLN cc_start: 0.8630 (mt0) cc_final: 0.8337 (mt0) REVERT: H 215 LYS cc_start: 0.5885 (tttp) cc_final: 0.5403 (mmtt) REVERT: H 224 ARG cc_start: 0.7722 (tpp-160) cc_final: 0.7409 (tpp-160) REVERT: H 272 MET cc_start: 0.8455 (mmm) cc_final: 0.7838 (mmp) REVERT: I 126 HIS cc_start: 0.6542 (m-70) cc_final: 0.6208 (m-70) REVERT: I 143 ASN cc_start: 0.7642 (m-40) cc_final: 0.7191 (m-40) REVERT: I 148 LEU cc_start: 0.8852 (mm) cc_final: 0.8502 (mm) REVERT: I 191 PRO cc_start: 0.8467 (Cg_exo) cc_final: 0.8167 (Cg_endo) REVERT: I 194 LYS cc_start: 0.9048 (mttt) cc_final: 0.8801 (mmmt) REVERT: J 48 CYS cc_start: 0.8585 (t) cc_final: 0.8243 (p) REVERT: J 155 CYS cc_start: 0.6483 (m) cc_final: 0.6268 (m) REVERT: M 94 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8251 (tp30) REVERT: N 84 MET cc_start: 0.8646 (mmp) cc_final: 0.8202 (tmm) REVERT: N 88 TYR cc_start: 0.8277 (m-10) cc_final: 0.7844 (m-10) REVERT: N 97 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8634 (mm) REVERT: N 98 TYR cc_start: 0.7797 (m-10) cc_final: 0.7347 (m-10) REVERT: O 84 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7605 (mm110) REVERT: O 91 GLU cc_start: 0.8965 (pm20) cc_final: 0.8582 (pp20) REVERT: O 92 GLU cc_start: 0.8476 (mt-10) cc_final: 0.6864 (tt0) REVERT: O 99 ARG cc_start: 0.7449 (mmm-85) cc_final: 0.6726 (tmm-80) REVERT: P 37 TYR cc_start: 0.8390 (m-10) cc_final: 0.8120 (m-10) REVERT: P 59 MET cc_start: 0.8972 (mmm) cc_final: 0.8765 (tpt) REVERT: P 62 MET cc_start: 0.9452 (mmm) cc_final: 0.9103 (tpp) REVERT: P 105 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8047 (pm20) REVERT: Q 90 MET cc_start: 0.8004 (mmp) cc_final: 0.7595 (mtt) REVERT: Q 134 ARG cc_start: 0.7924 (mtt180) cc_final: 0.7297 (ptm160) REVERT: R 35 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.8254 (mmm-85) REVERT: R 63 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7924 (tm-30) REVERT: R 91 LYS cc_start: 0.9181 (tppt) cc_final: 0.8950 (tptt) REVERT: S 56 GLU cc_start: 0.7659 (tt0) cc_final: 0.7407 (mt-10) REVERT: S 94 ASN cc_start: 0.8312 (t0) cc_final: 0.7788 (m110) REVERT: S 104 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7763 (tm-30) REVERT: T 59 MET cc_start: 0.8939 (tpp) cc_final: 0.8624 (tpp) REVERT: T 70 PHE cc_start: 0.9130 (t80) cc_final: 0.8649 (t80) REVERT: T 71 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8828 (mm-30) REVERT: T 79 ARG cc_start: 0.8421 (ttp-110) cc_final: 0.7942 (ptm-80) REVERT: T 96 THR cc_start: 0.8454 (m) cc_final: 0.8040 (p) REVERT: T 109 HIS cc_start: 0.7760 (m170) cc_final: 0.7539 (m90) outliers start: 112 outliers final: 55 residues processed: 685 average time/residue: 0.2713 time to fit residues: 305.2344 Evaluate side-chains 562 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 504 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain E residue 447 GLN Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 209 PHE Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 672 GLN Chi-restraints excluded: chain G residue 821 LEU Chi-restraints excluded: chain G residue 897 SER Chi-restraints excluded: chain G residue 1044 LEU Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain G residue 1110 LEU Chi-restraints excluded: chain H residue 276 CYS Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 124 PHE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 92 ARG Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 84 GLN Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 63 ARG Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 262 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 479 optimal weight: 10.0000 chunk 369 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 343 optimal weight: 30.0000 chunk 152 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 456 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN D 121 GLN D 422 GLN ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 706 HIS G1184 ASN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS M 108 ASN N 25 ASN ** N 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 GLN ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 HIS ** T 49 HIS ** 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 = 0.3915 r_free = 0.3915 target = 0.112879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072751 restraints weight = 109244.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.075185 restraints weight = 50648.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.076228 restraints weight = 28914.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.076674 restraints weight = 20571.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.076893 restraints weight = 17988.708| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 44424 Z= 0.178 Angle : 0.734 10.170 61158 Z= 0.395 Chirality : 0.049 0.281 6942 Planarity : 0.005 0.054 6851 Dihedral : 21.810 168.125 8318 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 2.95 % Allowed : 12.88 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.75 (0.12), residues: 4675 helix: -0.11 (0.11), residues: 2222 sheet: -0.69 (0.20), residues: 609 loop : -0.70 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 353 TYR 0.029 0.002 TYR T 40 PHE 0.026 0.002 PHE M 67 TRP 0.019 0.002 TRP J 540 HIS 0.008 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (44424) covalent geometry : angle 0.73419 / 0.40 (61158) hydrogen bonds : bond 0.05209 / 3.39 ( 1957) hydrogen bonds : angle 4.70209 / 3.27 ( 5316) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 549 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 SER cc_start: 0.8815 (t) cc_final: 0.8535 (t) REVERT: A 346 SER cc_start: 0.9324 (t) cc_final: 0.9021 (p) REVERT: C 273 ASP cc_start: 0.8221 (t0) cc_final: 0.7879 (t0) REVERT: D 35 ASP cc_start: 0.8429 (m-30) cc_final: 0.8013 (t0) REVERT: D 241 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8643 (p) REVERT: D 282 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7661 (tm-30) REVERT: D 313 ASN cc_start: 0.8677 (m-40) cc_final: 0.7944 (t0) REVERT: E 178 MET cc_start: 0.8550 (tmm) cc_final: 0.7966 (tmm) REVERT: E 201 LYS cc_start: 0.9137 (mttp) cc_final: 0.8867 (mtmm) REVERT: E 246 GLU cc_start: 0.7888 (pt0) cc_final: 0.7462 (pt0) REVERT: E 264 ASP cc_start: 0.7668 (t0) cc_final: 0.6969 (t0) REVERT: F 101 THR cc_start: 0.9320 (m) cc_final: 0.9111 (t) REVERT: F 144 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: F 291 ILE cc_start: 0.9238 (mt) cc_final: 0.9008 (tt) REVERT: G 929 LEU cc_start: 0.9157 (tt) cc_final: 0.8868 (mt) REVERT: G 1048 GLN cc_start: 0.8594 (mt0) cc_final: 0.8258 (mt0) REVERT: G 1136 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8307 (t80) REVERT: H 215 LYS cc_start: 0.6143 (tttp) cc_final: 0.5598 (mmtt) REVERT: H 272 MET cc_start: 0.8457 (mmm) cc_final: 0.7832 (mmp) REVERT: I 143 ASN cc_start: 0.7972 (m-40) cc_final: 0.7280 (m-40) REVERT: I 205 TYR cc_start: 0.8391 (t80) cc_final: 0.8053 (t80) REVERT: J 48 CYS cc_start: 0.8702 (t) cc_final: 0.8308 (p) REVERT: M 81 ASP cc_start: 0.8174 (t70) cc_final: 0.7818 (t70) REVERT: M 94 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8232 (tp30) REVERT: N 44 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8182 (mtmm) REVERT: N 62 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9028 (tp) REVERT: N 63 GLU cc_start: 0.9123 (pt0) cc_final: 0.8899 (pp20) REVERT: N 64 ASN cc_start: 0.8463 (p0) cc_final: 0.8038 (p0) REVERT: N 66 ILE cc_start: 0.9196 (mt) cc_final: 0.8987 (mt) REVERT: N 84 MET cc_start: 0.8556 (mmp) cc_final: 0.8188 (tmm) REVERT: N 88 TYR cc_start: 0.8209 (m-10) cc_final: 0.7901 (m-10) REVERT: N 98 TYR cc_start: 0.7700 (m-10) cc_final: 0.7333 (m-80) REVERT: O 33 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8016 (pp) REVERT: O 91 GLU cc_start: 0.8848 (pm20) cc_final: 0.8518 (pp20) REVERT: O 92 GLU cc_start: 0.8068 (mt-10) cc_final: 0.6453 (tt0) REVERT: O 99 ARG cc_start: 0.7382 (mmm-85) cc_final: 0.6756 (tmm-80) REVERT: P 59 MET cc_start: 0.8930 (mmm) cc_final: 0.8066 (mmm) REVERT: P 62 MET cc_start: 0.9383 (mmm) cc_final: 0.9037 (tpp) REVERT: P 65 PHE cc_start: 0.9370 (t80) cc_final: 0.9084 (t80) REVERT: P 105 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8112 (pm20) REVERT: Q 90 MET cc_start: 0.8010 (mmp) cc_final: 0.7502 (mtt) REVERT: Q 94 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7819 (mt-10) REVERT: Q 134 ARG cc_start: 0.7675 (mtt180) cc_final: 0.7261 (ptm160) REVERT: R 35 ARG cc_start: 0.8484 (ttp-110) cc_final: 0.7970 (tpp80) REVERT: R 44 LYS cc_start: 0.7862 (pptt) cc_final: 0.7652 (pptt) REVERT: R 51 TYR cc_start: 0.6556 (m-80) cc_final: 0.6254 (m-80) REVERT: R 63 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7924 (tm-30) REVERT: S 64 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8599 (tm-30) REVERT: S 94 ASN cc_start: 0.8341 (t0) cc_final: 0.7757 (m110) REVERT: S 100 VAL cc_start: 0.7526 (p) cc_final: 0.7309 (p) REVERT: T 44 VAL cc_start: 0.9462 (t) cc_final: 0.9091 (p) REVERT: T 47 GLN cc_start: 0.8995 (pt0) cc_final: 0.8523 (pp30) REVERT: T 59 MET cc_start: 0.8736 (tpp) cc_final: 0.8383 (tpp) REVERT: T 70 PHE cc_start: 0.9133 (t80) cc_final: 0.8592 (t80) REVERT: T 71 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8890 (mm-30) REVERT: T 79 ARG cc_start: 0.8522 (ttp-110) cc_final: 0.7838 (ptm-80) REVERT: T 95 GLN cc_start: 0.8862 (tt0) cc_final: 0.8632 (tp40) REVERT: T 113 GLU cc_start: 0.8383 (tt0) cc_final: 0.7614 (pp20) outliers start: 119 outliers final: 60 residues processed: 629 average time/residue: 0.2657 time to fit residues: 276.5220 Evaluate side-chains 557 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 491 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 628 ILE Chi-restraints excluded: chain G residue 649 MET Chi-restraints excluded: chain G residue 821 LEU Chi-restraints excluded: chain G residue 897 SER Chi-restraints excluded: chain G residue 1044 LEU Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain G residue 1136 TYR Chi-restraints excluded: chain H residue 276 CYS Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 124 PHE Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 ARG Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 63 ARG Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 228 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 263 optimal weight: 7.9990 chunk 329 optimal weight: 30.0000 chunk 336 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 310 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 299 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN D 146 GLN E 146 GLN ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 HIS ** G 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 672 GLN G 675 ASN G1027 ASN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS N 25 ASN ** N 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 GLN Q 85 GLN ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN T 49 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.113330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.073257 restraints weight = 109026.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.075352 restraints weight = 47829.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.076754 restraints weight = 27671.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.077601 restraints weight = 19251.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.078182 restraints weight = 15221.607| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44424 Z= 0.153 Angle : 0.692 8.869 61158 Z= 0.371 Chirality : 0.047 0.305 6942 Planarity : 0.004 0.056 6851 Dihedral : 21.888 169.386 8318 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.84 % Favored : 97.05 % Rotamer: Outliers : 2.80 % Allowed : 14.09 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4675 helix: 0.12 (0.11), residues: 2215 sheet: -0.80 (0.20), residues: 607 loop : -0.64 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 221 TYR 0.032 0.002 TYR S 57 PHE 0.023 0.001 PHE M 67 TRP 0.020 0.001 TRP G1061 HIS 0.009 0.001 HIS O 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (44424) covalent geometry : angle 0.69239 / 0.37 (61158) hydrogen bonds : bond 0.04695 / 3.04 ( 1957) hydrogen bonds : angle 4.51776 / 3.15 ( 5316) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 546 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 SER cc_start: 0.8700 (t) cc_final: 0.8460 (t) REVERT: A 346 SER cc_start: 0.9305 (t) cc_final: 0.8975 (p) REVERT: B 113 MET cc_start: 0.8464 (tpt) cc_final: 0.8217 (tpp) REVERT: B 114 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8063 (mt-10) REVERT: C 113 MET cc_start: 0.8228 (tpt) cc_final: 0.7925 (tpt) REVERT: C 273 ASP cc_start: 0.8272 (t0) cc_final: 0.7909 (t0) REVERT: C 278 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8206 (mm-30) REVERT: D 35 ASP cc_start: 0.8368 (m-30) cc_final: 0.7984 (t0) REVERT: D 241 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8691 (p) REVERT: D 282 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7754 (tm-30) REVERT: E 178 MET cc_start: 0.8629 (tmm) cc_final: 0.7902 (tmm) REVERT: E 246 GLU cc_start: 0.7810 (pt0) cc_final: 0.7360 (pt0) REVERT: E 264 ASP cc_start: 0.7716 (t0) cc_final: 0.6920 (t0) REVERT: F 162 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8159 (p) REVERT: F 291 ILE cc_start: 0.9249 (mt) cc_final: 0.9019 (tt) REVERT: F 354 LEU cc_start: 0.8804 (mp) cc_final: 0.8585 (mt) REVERT: G 739 LEU cc_start: 0.8033 (tp) cc_final: 0.7668 (mm) REVERT: G 929 LEU cc_start: 0.9127 (tt) cc_final: 0.8800 (mt) REVERT: G 1048 GLN cc_start: 0.8551 (mt0) cc_final: 0.8204 (mt0) REVERT: H 215 LYS cc_start: 0.6301 (tttp) cc_final: 0.5875 (mmtt) REVERT: H 224 ARG cc_start: 0.7766 (tpp-160) cc_final: 0.7527 (tpp-160) REVERT: H 272 MET cc_start: 0.8450 (mmm) cc_final: 0.7759 (mmp) REVERT: I 143 ASN cc_start: 0.8160 (m-40) cc_final: 0.7854 (m-40) REVERT: I 152 ARG cc_start: 0.7784 (tpp80) cc_final: 0.7456 (tpp80) REVERT: J 48 CYS cc_start: 0.8645 (t) cc_final: 0.8306 (p) REVERT: M 67 PHE cc_start: 0.9223 (t80) cc_final: 0.8634 (t80) REVERT: M 94 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8296 (tp30) REVERT: N 44 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8166 (mtmm) REVERT: N 62 LEU cc_start: 0.9243 (mm) cc_final: 0.8944 (tp) REVERT: N 64 ASN cc_start: 0.8480 (p0) cc_final: 0.8190 (p0) REVERT: N 68 ASP cc_start: 0.8522 (m-30) cc_final: 0.7856 (t0) REVERT: N 72 TYR cc_start: 0.7463 (m-80) cc_final: 0.6343 (m-80) REVERT: N 84 MET cc_start: 0.8628 (mmp) cc_final: 0.8217 (tmm) REVERT: N 88 TYR cc_start: 0.8315 (m-10) cc_final: 0.7902 (m-10) REVERT: N 98 TYR cc_start: 0.7632 (m-10) cc_final: 0.7213 (m-80) REVERT: O 33 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7963 (pp) REVERT: O 91 GLU cc_start: 0.8944 (pm20) cc_final: 0.8567 (pp20) REVERT: O 92 GLU cc_start: 0.8285 (mt-10) cc_final: 0.6624 (tt0) REVERT: O 99 ARG cc_start: 0.7427 (mmm-85) cc_final: 0.6938 (tmm-80) REVERT: P 59 MET cc_start: 0.8529 (mmm) cc_final: 0.8190 (mmm) REVERT: P 62 MET cc_start: 0.9496 (mmm) cc_final: 0.9214 (tpp) REVERT: P 105 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8223 (pm20) REVERT: Q 90 MET cc_start: 0.7972 (mmp) cc_final: 0.7580 (mtt) REVERT: Q 94 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7790 (mt-10) REVERT: Q 134 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7408 (ptm160) REVERT: R 35 ARG cc_start: 0.8291 (ttp-110) cc_final: 0.7935 (tpp80) REVERT: R 51 TYR cc_start: 0.6705 (m-80) cc_final: 0.6324 (m-80) REVERT: R 72 TYR cc_start: 0.8965 (m-80) cc_final: 0.8687 (m-80) REVERT: T 59 MET cc_start: 0.8685 (tpp) cc_final: 0.8351 (tpp) REVERT: T 70 PHE cc_start: 0.9191 (t80) cc_final: 0.8671 (t80) REVERT: T 71 GLU cc_start: 0.9356 (mm-30) cc_final: 0.8945 (mm-30) REVERT: T 79 ARG cc_start: 0.8279 (ttp-110) cc_final: 0.7939 (ptm-80) REVERT: T 95 GLN cc_start: 0.8819 (tt0) cc_final: 0.8461 (tp40) REVERT: T 113 GLU cc_start: 0.8463 (tt0) cc_final: 0.7560 (pp20) outliers start: 113 outliers final: 68 residues processed: 625 average time/residue: 0.2414 time to fit residues: 251.7811 Evaluate side-chains 557 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 485 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 398 SER Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 209 PHE Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 628 ILE Chi-restraints excluded: chain G residue 650 VAL Chi-restraints excluded: chain G residue 668 LEU Chi-restraints excluded: chain G residue 672 GLN Chi-restraints excluded: chain G residue 821 LEU Chi-restraints excluded: chain G residue 1044 LEU Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 124 PHE Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 463 GLU Chi-restraints excluded: chain J residue 468 ILE Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 577 ILE Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 63 ARG Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain S residue 38 ASN Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 330 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 14 optimal weight: 0.0470 chunk 3 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 323 optimal weight: 0.7980 chunk 384 optimal weight: 3.9990 overall best weight: 1.3480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 373 GLN ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 672 GLN G 675 ASN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 440 HIS M 108 ASN N 25 ASN ** N 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 GLN ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.112867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.072867 restraints weight = 108653.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.074953 restraints weight = 47733.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.076337 restraints weight = 27740.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.077224 restraints weight = 19240.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.077766 restraints weight = 15170.239| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 44424 Z= 0.166 Angle : 0.677 11.140 61158 Z= 0.362 Chirality : 0.046 0.271 6942 Planarity : 0.004 0.060 6851 Dihedral : 21.886 168.398 8317 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.71 % Rotamer: Outliers : 3.15 % Allowed : 14.69 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.43 (0.12), residues: 4675 helix: 0.26 (0.11), residues: 2212 sheet: -0.71 (0.20), residues: 576 loop : -0.65 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 213 TYR 0.024 0.002 TYR C 102 PHE 0.030 0.002 PHE M 67 TRP 0.021 0.001 TRP G1061 HIS 0.006 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (44424) covalent geometry : angle 0.67702 / 0.36 (61158) hydrogen bonds : bond 0.04496 / 2.90 ( 1957) hydrogen bonds : angle 4.43720 / 3.10 ( 5316) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 523 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 SER cc_start: 0.8677 (t) cc_final: 0.8447 (t) REVERT: A 320 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: A 346 SER cc_start: 0.9314 (t) cc_final: 0.8985 (p) REVERT: B 114 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8056 (mt-10) REVERT: B 260 MET cc_start: 0.8507 (ttp) cc_final: 0.8080 (ttt) REVERT: C 61 MET cc_start: 0.8330 (mmm) cc_final: 0.8082 (mmm) REVERT: C 113 MET cc_start: 0.8233 (tpt) cc_final: 0.7999 (tpt) REVERT: C 273 ASP cc_start: 0.8274 (t0) cc_final: 0.7893 (t0) REVERT: D 35 ASP cc_start: 0.8276 (m-30) cc_final: 0.7969 (t0) REVERT: D 282 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7815 (tm-30) REVERT: E 149 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6352 (tmm160) REVERT: E 178 MET cc_start: 0.8652 (tmm) cc_final: 0.8047 (tmm) REVERT: E 246 GLU cc_start: 0.7798 (pt0) cc_final: 0.7354 (pt0) REVERT: E 264 ASP cc_start: 0.7659 (t0) cc_final: 0.6973 (t0) REVERT: F 162 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8172 (p) REVERT: F 291 ILE cc_start: 0.9265 (mt) cc_final: 0.9047 (tt) REVERT: G 929 LEU cc_start: 0.9127 (tt) cc_final: 0.8820 (mt) REVERT: G 1048 GLN cc_start: 0.8553 (mt0) cc_final: 0.8204 (mt0) REVERT: G 1148 ASP cc_start: 0.8212 (t0) cc_final: 0.7620 (p0) REVERT: H 215 LYS cc_start: 0.6501 (tttp) cc_final: 0.6042 (mmtt) REVERT: H 224 ARG cc_start: 0.7788 (tpp-160) cc_final: 0.7499 (tpp-160) REVERT: H 272 MET cc_start: 0.8467 (mmm) cc_final: 0.7782 (mmp) REVERT: I 152 ARG cc_start: 0.7800 (tpp80) cc_final: 0.7394 (tpp80) REVERT: J 48 CYS cc_start: 0.8611 (t) cc_final: 0.8303 (p) REVERT: J 148 MET cc_start: 0.8828 (tpp) cc_final: 0.8626 (tpp) REVERT: J 233 HIS cc_start: 0.8097 (OUTLIER) cc_final: 0.7583 (p-80) REVERT: J 565 LEU cc_start: 0.7713 (tp) cc_final: 0.7267 (pp) REVERT: M 94 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8367 (tp30) REVERT: N 62 LEU cc_start: 0.9202 (mm) cc_final: 0.8931 (tp) REVERT: N 84 MET cc_start: 0.8495 (mmp) cc_final: 0.8074 (tmm) REVERT: N 88 TYR cc_start: 0.8290 (m-10) cc_final: 0.7775 (m-10) REVERT: N 98 TYR cc_start: 0.7559 (m-10) cc_final: 0.7158 (m-80) REVERT: O 33 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7986 (pp) REVERT: O 61 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7323 (tm-30) REVERT: O 63 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8592 (pp) REVERT: O 91 GLU cc_start: 0.8984 (pm20) cc_final: 0.8606 (pp20) REVERT: O 92 GLU cc_start: 0.8216 (mt-10) cc_final: 0.6630 (tt0) REVERT: O 99 ARG cc_start: 0.7329 (mmm-85) cc_final: 0.7057 (ttt-90) REVERT: P 59 MET cc_start: 0.8550 (mmm) cc_final: 0.8344 (mmm) REVERT: P 62 MET cc_start: 0.9476 (mmm) cc_final: 0.9216 (tpp) REVERT: P 105 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8196 (pm20) REVERT: Q 90 MET cc_start: 0.7988 (mmp) cc_final: 0.7549 (mtt) REVERT: Q 134 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7392 (ptm160) REVERT: R 44 LYS cc_start: 0.7439 (pptt) cc_final: 0.7012 (pptt) REVERT: R 51 TYR cc_start: 0.6651 (m-80) cc_final: 0.6408 (m-80) REVERT: R 63 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7771 (tm-30) REVERT: R 72 TYR cc_start: 0.8956 (m-80) cc_final: 0.8737 (m-80) REVERT: R 90 LEU cc_start: 0.8685 (mt) cc_final: 0.8342 (mt) REVERT: R 91 LYS cc_start: 0.9192 (tptt) cc_final: 0.8555 (tptt) REVERT: T 39 ILE cc_start: 0.8293 (pt) cc_final: 0.8033 (pt) REVERT: T 46 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8745 (mmmt) REVERT: T 59 MET cc_start: 0.8700 (tpp) cc_final: 0.8401 (tpp) REVERT: T 70 PHE cc_start: 0.9181 (t80) cc_final: 0.8720 (t80) REVERT: T 71 GLU cc_start: 0.9396 (mm-30) cc_final: 0.8977 (mm-30) REVERT: T 79 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.7933 (ptm-80) REVERT: T 95 GLN cc_start: 0.8858 (tt0) cc_final: 0.8467 (tp40) REVERT: T 113 GLU cc_start: 0.8447 (tt0) cc_final: 0.7516 (pp20) outliers start: 127 outliers final: 76 residues processed: 612 average time/residue: 0.2635 time to fit residues: 269.0089 Evaluate side-chains 568 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 486 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 359 MET Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 305 ASP Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 398 SER Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 650 VAL Chi-restraints excluded: chain G residue 668 LEU Chi-restraints excluded: chain G residue 672 GLN Chi-restraints excluded: chain G residue 821 LEU Chi-restraints excluded: chain G residue 1044 LEU Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain G residue 1110 LEU Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 124 PHE Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 233 HIS Chi-restraints excluded: chain J residue 444 VAL Chi-restraints excluded: chain J residue 463 GLU Chi-restraints excluded: chain J residue 468 ILE Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 577 ILE Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain S residue 38 ASN Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 379 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 486 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 398 optimal weight: 30.0000 chunk 454 optimal weight: 40.0000 chunk 229 optimal weight: 0.0570 chunk 187 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 313 ASN ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 675 ASN G1027 ASN ** G1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN N 25 ASN ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 108 ASN R 75 HIS ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.113132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.073070 restraints weight = 108767.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.075143 restraints weight = 47824.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.076556 restraints weight = 27797.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.077422 restraints weight = 19288.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.077973 restraints weight = 15272.357| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 44424 Z= 0.150 Angle : 0.663 9.835 61158 Z= 0.353 Chirality : 0.045 0.276 6942 Planarity : 0.004 0.078 6851 Dihedral : 21.854 168.133 8316 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.02 % Favored : 96.88 % Rotamer: Outliers : 2.93 % Allowed : 15.73 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.38 (0.12), residues: 4675 helix: 0.34 (0.11), residues: 2218 sheet: -0.76 (0.20), residues: 582 loop : -0.64 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 213 TYR 0.025 0.001 TYR J 564 PHE 0.031 0.001 PHE M 67 TRP 0.021 0.001 TRP G1061 HIS 0.005 0.001 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (44424) covalent geometry : angle 0.66262 / 0.35 (61158) hydrogen bonds : bond 0.04302 / 2.77 ( 1957) hydrogen bonds : angle 4.36564 / 3.05 ( 5316) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 528 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 SER cc_start: 0.8661 (t) cc_final: 0.8437 (t) REVERT: A 320 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7596 (mm-30) REVERT: A 346 SER cc_start: 0.9300 (t) cc_final: 0.8975 (p) REVERT: B 114 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8173 (mt-10) REVERT: C 61 MET cc_start: 0.8279 (mmm) cc_final: 0.7892 (mmm) REVERT: C 273 ASP cc_start: 0.8308 (t0) cc_final: 0.7948 (t0) REVERT: D 35 ASP cc_start: 0.8227 (m-30) cc_final: 0.8002 (t70) REVERT: D 248 ASP cc_start: 0.7961 (m-30) cc_final: 0.7682 (m-30) REVERT: D 282 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7827 (tm-30) REVERT: E 149 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6182 (tmm-80) REVERT: E 178 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8020 (tmm) REVERT: E 406 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9238 (mp) REVERT: F 46 MET cc_start: 0.8052 (mtp) cc_final: 0.7801 (mtp) REVERT: F 162 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8195 (p) REVERT: F 291 ILE cc_start: 0.9253 (mt) cc_final: 0.9032 (tt) REVERT: G 526 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6909 (tpt) REVERT: G 929 LEU cc_start: 0.9117 (tt) cc_final: 0.8822 (mt) REVERT: G 1048 GLN cc_start: 0.8527 (mt0) cc_final: 0.8173 (mt0) REVERT: G 1148 ASP cc_start: 0.8247 (t0) cc_final: 0.7600 (p0) REVERT: G 1247 MET cc_start: 0.6339 (ptt) cc_final: 0.5907 (ttp) REVERT: H 215 LYS cc_start: 0.6553 (tttp) cc_final: 0.6121 (mmtt) REVERT: H 224 ARG cc_start: 0.7787 (tpp-160) cc_final: 0.7519 (tpp-160) REVERT: H 272 MET cc_start: 0.8465 (mmm) cc_final: 0.7804 (mmp) REVERT: I 144 LEU cc_start: 0.8238 (mt) cc_final: 0.7938 (mt) REVERT: I 145 LYS cc_start: 0.8988 (ttmm) cc_final: 0.8730 (pttm) REVERT: J 48 CYS cc_start: 0.8569 (t) cc_final: 0.8267 (p) REVERT: J 148 MET cc_start: 0.8852 (tpp) cc_final: 0.8632 (tpp) REVERT: J 481 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8506 (tptt) REVERT: M 94 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8337 (tp30) REVERT: N 62 LEU cc_start: 0.9247 (mm) cc_final: 0.9016 (tp) REVERT: N 68 ASP cc_start: 0.8505 (m-30) cc_final: 0.7948 (t0) REVERT: N 84 MET cc_start: 0.8494 (mmp) cc_final: 0.8072 (tmm) REVERT: N 88 TYR cc_start: 0.8389 (m-10) cc_final: 0.7883 (m-10) REVERT: N 98 TYR cc_start: 0.7515 (m-10) cc_final: 0.7151 (m-80) REVERT: O 56 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8677 (mm-30) REVERT: O 61 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7368 (tm-30) REVERT: O 63 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8605 (pp) REVERT: O 91 GLU cc_start: 0.9000 (pm20) cc_final: 0.8574 (pp20) REVERT: O 92 GLU cc_start: 0.8192 (mt-10) cc_final: 0.6611 (tt0) REVERT: O 99 ARG cc_start: 0.7382 (mmm-85) cc_final: 0.7170 (ttt-90) REVERT: P 62 MET cc_start: 0.9479 (mmm) cc_final: 0.8918 (tpp) REVERT: P 105 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8148 (pm20) REVERT: Q 90 MET cc_start: 0.7874 (mmp) cc_final: 0.7547 (mtt) REVERT: Q 134 ARG cc_start: 0.7989 (mtt180) cc_final: 0.7461 (ptm160) REVERT: R 44 LYS cc_start: 0.7604 (pptt) cc_final: 0.7250 (pptt) REVERT: R 50 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7779 (mm) REVERT: R 72 TYR cc_start: 0.8992 (m-80) cc_final: 0.8762 (m-80) REVERT: R 90 LEU cc_start: 0.8702 (mt) cc_final: 0.8486 (mt) REVERT: R 91 LYS cc_start: 0.9195 (tptt) cc_final: 0.8507 (tptt) REVERT: S 92 GLU cc_start: 0.8608 (mp0) cc_final: 0.8237 (mt-10) REVERT: T 39 ILE cc_start: 0.8359 (pt) cc_final: 0.8065 (pt) REVERT: T 47 GLN cc_start: 0.8973 (pt0) cc_final: 0.8558 (pp30) REVERT: T 59 MET cc_start: 0.8594 (tpp) cc_final: 0.8306 (tpp) REVERT: T 70 PHE cc_start: 0.9160 (t80) cc_final: 0.8729 (t80) REVERT: T 71 GLU cc_start: 0.9436 (mm-30) cc_final: 0.8986 (mm-30) REVERT: T 79 ARG cc_start: 0.8397 (ttp-110) cc_final: 0.7960 (ptm-80) REVERT: T 95 GLN cc_start: 0.8823 (tt0) cc_final: 0.8428 (tp40) REVERT: T 113 GLU cc_start: 0.8433 (tt0) cc_final: 0.7505 (pp20) outliers start: 118 outliers final: 81 residues processed: 612 average time/residue: 0.2623 time to fit residues: 266.0769 Evaluate side-chains 574 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 484 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 359 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 398 SER Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 526 MET Chi-restraints excluded: chain G residue 593 PHE Chi-restraints excluded: chain G residue 650 VAL Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 1044 LEU Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain G residue 1110 LEU Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1235 LEU Chi-restraints excluded: chain G residue 1245 GLN Chi-restraints excluded: chain I residue 124 PHE Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 444 VAL Chi-restraints excluded: chain J residue 463 GLU Chi-restraints excluded: chain J residue 468 ILE Chi-restraints excluded: chain J residue 481 LYS Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 577 ILE Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain S residue 38 ASN Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 391 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 113 optimal weight: 0.4980 chunk 448 optimal weight: 20.0000 chunk 360 optimal weight: 2.9990 chunk 339 optimal weight: 0.9990 chunk 344 optimal weight: 7.9990 chunk 416 optimal weight: 40.0000 chunk 356 optimal weight: 0.0270 chunk 395 optimal weight: 50.0000 overall best weight: 1.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 675 ASN ** G1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 HIS ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.112260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.072018 restraints weight = 107903.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.074109 restraints weight = 48104.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.075429 restraints weight = 28078.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.076291 restraints weight = 19771.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.076820 restraints weight = 15709.150| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 44424 Z= 0.183 Angle : 0.677 11.044 61158 Z= 0.358 Chirality : 0.046 0.438 6942 Planarity : 0.004 0.060 6851 Dihedral : 21.839 167.737 8316 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.42 % Favored : 96.47 % Rotamer: Outliers : 3.15 % Allowed : 16.05 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.39 (0.12), residues: 4675 helix: 0.37 (0.11), residues: 2223 sheet: -0.85 (0.19), residues: 611 loop : -0.66 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG O 35 TYR 0.037 0.002 TYR S 57 PHE 0.030 0.001 PHE M 67 TRP 0.020 0.001 TRP G1061 HIS 0.005 0.001 HIS F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (44424) covalent geometry : angle 0.67691 / 0.36 (61158) hydrogen bonds : bond 0.04312 / 2.78 ( 1957) hydrogen bonds : angle 4.38496 / 3.06 ( 5316) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 498 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 SER cc_start: 0.8618 (t) cc_final: 0.8408 (t) REVERT: A 320 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: A 346 SER cc_start: 0.9329 (t) cc_final: 0.9009 (p) REVERT: B 114 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8167 (mt-10) REVERT: C 273 ASP cc_start: 0.8354 (t0) cc_final: 0.8005 (t0) REVERT: C 371 MET cc_start: 0.8754 (tpp) cc_final: 0.8206 (mmt) REVERT: D 35 ASP cc_start: 0.8248 (m-30) cc_final: 0.8012 (t0) REVERT: D 248 ASP cc_start: 0.7975 (m-30) cc_final: 0.7725 (m-30) REVERT: D 282 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7839 (tm-30) REVERT: D 313 ASN cc_start: 0.8444 (t0) cc_final: 0.8238 (t0) REVERT: E 149 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6349 (tmm-80) REVERT: E 178 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8032 (tmm) REVERT: F 162 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8234 (p) REVERT: F 291 ILE cc_start: 0.9268 (mt) cc_final: 0.9066 (tt) REVERT: F 354 LEU cc_start: 0.9004 (mt) cc_final: 0.8683 (mt) REVERT: G 929 LEU cc_start: 0.9139 (tt) cc_final: 0.8815 (mt) REVERT: G 1048 GLN cc_start: 0.8554 (mt0) cc_final: 0.8192 (mt0) REVERT: G 1126 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.7842 (mtm) REVERT: G 1148 ASP cc_start: 0.8266 (t0) cc_final: 0.7618 (p0) REVERT: G 1247 MET cc_start: 0.6411 (ptt) cc_final: 0.6021 (ttp) REVERT: H 215 LYS cc_start: 0.6586 (tttp) cc_final: 0.6142 (mmtt) REVERT: H 224 ARG cc_start: 0.7807 (tpp-160) cc_final: 0.7527 (tpp-160) REVERT: H 272 MET cc_start: 0.8496 (mmm) cc_final: 0.7804 (mmp) REVERT: I 145 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8675 (pttm) REVERT: J 48 CYS cc_start: 0.8569 (t) cc_final: 0.8263 (p) REVERT: J 107 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6654 (pt0) REVERT: J 148 MET cc_start: 0.8859 (tpp) cc_final: 0.8639 (tpp) REVERT: J 481 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8509 (tptt) REVERT: M 94 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8401 (tp30) REVERT: N 68 ASP cc_start: 0.8525 (m-30) cc_final: 0.7957 (t0) REVERT: N 84 MET cc_start: 0.8497 (mmp) cc_final: 0.8077 (tmm) REVERT: N 88 TYR cc_start: 0.8342 (m-10) cc_final: 0.7844 (m-10) REVERT: N 98 TYR cc_start: 0.7553 (m-10) cc_final: 0.7243 (m-80) REVERT: O 56 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8693 (mm-30) REVERT: O 61 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7451 (tm-30) REVERT: O 63 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8597 (pp) REVERT: O 91 GLU cc_start: 0.9012 (pm20) cc_final: 0.8529 (pp20) REVERT: O 92 GLU cc_start: 0.8164 (mt-10) cc_final: 0.6366 (mt-10) REVERT: O 102 ILE cc_start: 0.7909 (mp) cc_final: 0.7634 (mm) REVERT: P 59 MET cc_start: 0.8730 (mmm) cc_final: 0.8409 (mmm) REVERT: P 62 MET cc_start: 0.9470 (mmm) cc_final: 0.9219 (tpp) REVERT: P 105 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8129 (pm20) REVERT: Q 90 MET cc_start: 0.7871 (mmp) cc_final: 0.7556 (mtt) REVERT: Q 134 ARG cc_start: 0.8011 (mtt180) cc_final: 0.7497 (ptm160) REVERT: R 35 ARG cc_start: 0.8165 (mmm-85) cc_final: 0.7692 (ttm-80) REVERT: R 44 LYS cc_start: 0.7773 (pptt) cc_final: 0.7493 (pptt) REVERT: R 50 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7721 (mm) REVERT: R 72 TYR cc_start: 0.9027 (m-80) cc_final: 0.8810 (m-80) REVERT: S 92 GLU cc_start: 0.8580 (mp0) cc_final: 0.8247 (mt-10) REVERT: S 100 VAL cc_start: 0.7393 (p) cc_final: 0.7166 (p) REVERT: T 39 ILE cc_start: 0.8439 (pt) cc_final: 0.8148 (pt) REVERT: T 59 MET cc_start: 0.8565 (tpp) cc_final: 0.8295 (tpp) REVERT: T 70 PHE cc_start: 0.9142 (t80) cc_final: 0.8719 (t80) REVERT: T 71 GLU cc_start: 0.9438 (mm-30) cc_final: 0.9003 (mm-30) REVERT: T 79 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.7939 (ptm-80) REVERT: T 95 GLN cc_start: 0.8820 (tt0) cc_final: 0.8443 (tp40) REVERT: T 113 GLU cc_start: 0.8418 (tt0) cc_final: 0.7521 (pp20) outliers start: 127 outliers final: 84 residues processed: 585 average time/residue: 0.2532 time to fit residues: 245.0129 Evaluate side-chains 565 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 472 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 359 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 398 SER Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 209 PHE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 593 PHE Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 1044 LEU Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1126 MET Chi-restraints excluded: chain G residue 1235 LEU Chi-restraints excluded: chain G residue 1245 GLN Chi-restraints excluded: chain I residue 124 PHE Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 233 HIS Chi-restraints excluded: chain J residue 252 ILE Chi-restraints excluded: chain J residue 444 VAL Chi-restraints excluded: chain J residue 463 GLU Chi-restraints excluded: chain J residue 468 ILE Chi-restraints excluded: chain J residue 481 LYS Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 577 ILE Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 119 ILE Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain S residue 38 ASN Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 379 optimal weight: 7.9990 chunk 310 optimal weight: 1.9990 chunk 339 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 420 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 353 optimal weight: 0.5980 chunk 314 optimal weight: 0.9990 chunk 347 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 429 HIS ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 675 ASN ** G1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 544 HIS M 108 ASN N 25 ASN N 27 GLN O 31 HIS ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 HIS ** S 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.113123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.073701 restraints weight = 108759.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.076546 restraints weight = 48051.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.076755 restraints weight = 23125.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.077189 restraints weight = 19964.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.077227 restraints weight = 18815.473| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 44424 Z= 0.149 Angle : 0.660 12.987 61158 Z= 0.349 Chirality : 0.045 0.294 6942 Planarity : 0.004 0.063 6851 Dihedral : 21.814 167.666 8316 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.71 % Rotamer: Outliers : 2.83 % Allowed : 16.65 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.28 (0.12), residues: 4675 helix: 0.47 (0.11), residues: 2220 sheet: -0.90 (0.20), residues: 579 loop : -0.59 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 213 TYR 0.033 0.001 TYR N 72 PHE 0.027 0.001 PHE M 67 TRP 0.021 0.001 TRP G1061 HIS 0.004 0.001 HIS F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (44424) covalent geometry : angle 0.65996 / 0.35 (61158) hydrogen bonds : bond 0.04057 / 2.62 ( 1957) hydrogen bonds : angle 4.33909 / 3.04 ( 5316) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 521 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8751 (mmm) cc_final: 0.7701 (mmm) REVERT: A 99 SER cc_start: 0.8530 (t) cc_final: 0.8308 (t) REVERT: A 211 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8522 (p) REVERT: A 320 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: A 346 SER cc_start: 0.9286 (t) cc_final: 0.8974 (p) REVERT: B 186 GLU cc_start: 0.7150 (pp20) cc_final: 0.6659 (pp20) REVERT: C 273 ASP cc_start: 0.8382 (t0) cc_final: 0.8027 (t0) REVERT: C 371 MET cc_start: 0.8795 (tpp) cc_final: 0.8213 (mmt) REVERT: D 35 ASP cc_start: 0.8332 (m-30) cc_final: 0.8067 (t0) REVERT: D 248 ASP cc_start: 0.7984 (m-30) cc_final: 0.7743 (m-30) REVERT: D 282 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7816 (tm-30) REVERT: D 313 ASN cc_start: 0.8488 (t0) cc_final: 0.8260 (t0) REVERT: E 149 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6325 (tmm-80) REVERT: E 178 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8046 (tmm) REVERT: E 197 LYS cc_start: 0.8667 (ttpp) cc_final: 0.8410 (mtpt) REVERT: E 264 ASP cc_start: 0.8014 (t0) cc_final: 0.7296 (t0) REVERT: F 162 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8244 (p) REVERT: F 354 LEU cc_start: 0.8990 (mt) cc_final: 0.8661 (mt) REVERT: G 739 LEU cc_start: 0.7878 (tp) cc_final: 0.7441 (mm) REVERT: G 929 LEU cc_start: 0.9110 (tt) cc_final: 0.8802 (mt) REVERT: G 1048 GLN cc_start: 0.8519 (mt0) cc_final: 0.7767 (mp10) REVERT: G 1126 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.7810 (mtm) REVERT: G 1148 ASP cc_start: 0.8265 (t0) cc_final: 0.7621 (p0) REVERT: G 1247 MET cc_start: 0.6640 (ptt) cc_final: 0.6345 (ttp) REVERT: H 215 LYS cc_start: 0.6735 (tttp) cc_final: 0.6251 (mmtt) REVERT: H 224 ARG cc_start: 0.7926 (tpp-160) cc_final: 0.7552 (tpp-160) REVERT: H 272 MET cc_start: 0.8567 (mmm) cc_final: 0.7840 (mmp) REVERT: I 145 LYS cc_start: 0.8869 (ttmm) cc_final: 0.8644 (pttm) REVERT: J 48 CYS cc_start: 0.8692 (t) cc_final: 0.8271 (p) REVERT: J 107 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6685 (pt0) REVERT: J 148 MET cc_start: 0.8953 (tpp) cc_final: 0.8719 (tpp) REVERT: J 481 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8494 (tptt) REVERT: M 74 ILE cc_start: 0.9141 (mm) cc_final: 0.8911 (mm) REVERT: M 94 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8421 (tp30) REVERT: N 30 THR cc_start: 0.8747 (p) cc_final: 0.8500 (t) REVERT: N 63 GLU cc_start: 0.9237 (pp20) cc_final: 0.8910 (pp20) REVERT: N 68 ASP cc_start: 0.8481 (m-30) cc_final: 0.7984 (t0) REVERT: N 84 MET cc_start: 0.8509 (mmp) cc_final: 0.8197 (tmm) REVERT: N 88 TYR cc_start: 0.8301 (m-10) cc_final: 0.7927 (m-10) REVERT: N 91 LYS cc_start: 0.9335 (mmmm) cc_final: 0.9068 (mmmm) REVERT: N 98 TYR cc_start: 0.7626 (m-10) cc_final: 0.7341 (m-80) REVERT: O 56 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8682 (mm-30) REVERT: O 63 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8571 (pp) REVERT: O 91 GLU cc_start: 0.8995 (pm20) cc_final: 0.8372 (pp20) REVERT: O 92 GLU cc_start: 0.7925 (mt-10) cc_final: 0.6403 (tt0) REVERT: O 102 ILE cc_start: 0.7927 (mp) cc_final: 0.7691 (mm) REVERT: P 59 MET cc_start: 0.8648 (mmm) cc_final: 0.8377 (mmm) REVERT: P 102 LEU cc_start: 0.8325 (mt) cc_final: 0.7459 (tt) REVERT: P 105 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8078 (pm20) REVERT: Q 90 MET cc_start: 0.7860 (mmp) cc_final: 0.7407 (mtt) REVERT: Q 94 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7716 (mt-10) REVERT: Q 97 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7890 (pp20) REVERT: Q 122 LYS cc_start: 0.8626 (pttm) cc_final: 0.7794 (tppt) REVERT: Q 134 ARG cc_start: 0.7893 (mtt180) cc_final: 0.7469 (ptm160) REVERT: R 35 ARG cc_start: 0.8211 (mmm-85) cc_final: 0.7797 (ttm-80) REVERT: R 50 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7715 (mm) REVERT: R 72 TYR cc_start: 0.9060 (m-80) cc_final: 0.8844 (m-80) REVERT: S 92 GLU cc_start: 0.8412 (mp0) cc_final: 0.8154 (mt-10) REVERT: S 100 VAL cc_start: 0.7536 (p) cc_final: 0.7316 (p) REVERT: T 39 ILE cc_start: 0.8583 (pt) cc_final: 0.8363 (pt) REVERT: T 46 LYS cc_start: 0.8963 (mtpp) cc_final: 0.8687 (mmmt) REVERT: T 59 MET cc_start: 0.8514 (tpp) cc_final: 0.8230 (tpp) REVERT: T 70 PHE cc_start: 0.9105 (t80) cc_final: 0.8630 (t80) REVERT: T 71 GLU cc_start: 0.9422 (mm-30) cc_final: 0.8963 (mm-30) REVERT: T 79 ARG cc_start: 0.8397 (ttp-110) cc_final: 0.7979 (ptm-80) REVERT: T 95 GLN cc_start: 0.8825 (tt0) cc_final: 0.8406 (tp40) REVERT: T 99 ARG cc_start: 0.8664 (tpp80) cc_final: 0.8290 (mtt-85) REVERT: T 113 GLU cc_start: 0.8397 (tt0) cc_final: 0.7530 (pp20) outliers start: 114 outliers final: 81 residues processed: 597 average time/residue: 0.2609 time to fit residues: 257.4657 Evaluate side-chains 571 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 480 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 398 SER Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 209 PHE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 1044 LEU Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1126 MET Chi-restraints excluded: chain G residue 1137 MET Chi-restraints excluded: chain G residue 1235 LEU Chi-restraints excluded: chain G residue 1245 GLN Chi-restraints excluded: chain I residue 124 PHE Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 233 HIS Chi-restraints excluded: chain J residue 252 ILE Chi-restraints excluded: chain J residue 444 VAL Chi-restraints excluded: chain J residue 463 GLU Chi-restraints excluded: chain J residue 468 ILE Chi-restraints excluded: chain J residue 481 LYS Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 577 ILE Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain O residue 25 PHE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain S residue 38 ASN Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 4 optimal weight: 2.9990 chunk 418 optimal weight: 50.0000 chunk 366 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 302 optimal weight: 4.9990 chunk 325 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 396 optimal weight: 50.0000 chunk 39 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 675 ASN ** G1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN N 25 ASN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 HIS ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 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 = 0.3895 r_free = 0.3895 target = 0.111918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.072924 restraints weight = 106034.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075300 restraints weight = 49014.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.075662 restraints weight = 24881.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.076358 restraints weight = 19669.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.076330 restraints weight = 17177.925| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 44424 Z= 0.183 Angle : 0.675 13.430 61158 Z= 0.356 Chirality : 0.046 0.335 6942 Planarity : 0.004 0.079 6851 Dihedral : 21.807 167.656 8316 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 2.80 % Allowed : 17.22 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.30 (0.12), residues: 4675 helix: 0.49 (0.11), residues: 2227 sheet: -0.94 (0.20), residues: 594 loop : -0.63 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG N 55 TYR 0.030 0.002 TYR S 57 PHE 0.022 0.001 PHE M 67 TRP 0.019 0.001 TRP G1061 HIS 0.006 0.001 HIS O 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (44424) covalent geometry : angle 0.67544 / 0.36 (61158) hydrogen bonds : bond 0.04140 / 2.68 ( 1957) hydrogen bonds : angle 4.35823 / 3.05 ( 5316) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 487 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8855 (mmm) cc_final: 0.7937 (mmm) REVERT: A 99 SER cc_start: 0.8565 (t) cc_final: 0.8351 (t) REVERT: A 211 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8553 (p) REVERT: A 320 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7493 (mm-30) REVERT: A 346 SER cc_start: 0.9311 (t) cc_final: 0.8973 (p) REVERT: B 186 GLU cc_start: 0.7176 (pp20) cc_final: 0.6681 (pp20) REVERT: B 278 GLU cc_start: 0.7870 (tp30) cc_final: 0.7218 (tp30) REVERT: B 285 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8575 (tppt) REVERT: C 273 ASP cc_start: 0.8470 (t0) cc_final: 0.8145 (t0) REVERT: C 306 MET cc_start: 0.8661 (mmm) cc_final: 0.8393 (mmm) REVERT: C 371 MET cc_start: 0.8798 (tpp) cc_final: 0.8183 (mmt) REVERT: D 35 ASP cc_start: 0.8341 (m-30) cc_final: 0.8063 (t0) REVERT: D 248 ASP cc_start: 0.8019 (m-30) cc_final: 0.7796 (m-30) REVERT: D 282 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7904 (tm-30) REVERT: D 313 ASN cc_start: 0.8486 (t0) cc_final: 0.8113 (t0) REVERT: E 149 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6336 (tmm-80) REVERT: E 178 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8056 (tmm) REVERT: E 197 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8444 (mtpt) REVERT: E 218 MET cc_start: 0.5952 (mpp) cc_final: 0.5723 (mpp) REVERT: E 264 ASP cc_start: 0.8087 (t0) cc_final: 0.7395 (t0) REVERT: F 46 MET cc_start: 0.7990 (mtp) cc_final: 0.7567 (mtp) REVERT: F 162 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8263 (p) REVERT: G 739 LEU cc_start: 0.7892 (tp) cc_final: 0.7432 (mm) REVERT: G 929 LEU cc_start: 0.9133 (tt) cc_final: 0.8788 (mt) REVERT: G 1048 GLN cc_start: 0.8551 (mt0) cc_final: 0.7790 (mp10) REVERT: G 1126 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.7784 (mtm) REVERT: G 1148 ASP cc_start: 0.8292 (t0) cc_final: 0.7645 (p0) REVERT: H 215 LYS cc_start: 0.6695 (tttp) cc_final: 0.6233 (mmtt) REVERT: H 224 ARG cc_start: 0.7961 (tpp-160) cc_final: 0.7587 (tpp-160) REVERT: H 272 MET cc_start: 0.8609 (mmm) cc_final: 0.7864 (mmp) REVERT: I 145 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8478 (pttm) REVERT: I 152 ARG cc_start: 0.7745 (tpp80) cc_final: 0.7268 (tpp-160) REVERT: I 187 ASN cc_start: 0.8821 (m-40) cc_final: 0.8587 (m-40) REVERT: J 48 CYS cc_start: 0.8589 (t) cc_final: 0.8243 (p) REVERT: J 107 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6675 (pt0) REVERT: J 148 MET cc_start: 0.8932 (tpp) cc_final: 0.8701 (tpp) REVERT: J 481 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8519 (tptt) REVERT: M 94 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8171 (tp30) REVERT: N 30 THR cc_start: 0.8832 (p) cc_final: 0.8607 (t) REVERT: N 68 ASP cc_start: 0.8395 (m-30) cc_final: 0.8036 (t0) REVERT: N 84 MET cc_start: 0.8490 (mmp) cc_final: 0.8290 (tmm) REVERT: N 98 TYR cc_start: 0.7705 (m-10) cc_final: 0.7422 (m-80) REVERT: O 33 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8223 (pp) REVERT: O 56 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8685 (mm-30) REVERT: O 63 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8500 (pp) REVERT: O 91 GLU cc_start: 0.8959 (pm20) cc_final: 0.8331 (pp20) REVERT: O 92 GLU cc_start: 0.7882 (mt-10) cc_final: 0.6400 (tt0) REVERT: O 102 ILE cc_start: 0.7912 (mp) cc_final: 0.7683 (mm) REVERT: P 59 MET cc_start: 0.8595 (mmm) cc_final: 0.8352 (mmm) REVERT: P 62 MET cc_start: 0.9174 (tpp) cc_final: 0.8656 (tpp) REVERT: P 105 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8061 (pm20) REVERT: Q 90 MET cc_start: 0.7851 (mmp) cc_final: 0.7388 (mtt) REVERT: Q 94 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7814 (mt-10) REVERT: Q 122 LYS cc_start: 0.8661 (pttm) cc_final: 0.7798 (tppt) REVERT: Q 134 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7474 (ptm160) REVERT: R 35 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.7815 (ttm-80) REVERT: R 50 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7727 (mm) REVERT: R 72 TYR cc_start: 0.9036 (m-80) cc_final: 0.8804 (m-80) REVERT: S 92 GLU cc_start: 0.8380 (mp0) cc_final: 0.8101 (mt-10) REVERT: S 100 VAL cc_start: 0.7466 (p) cc_final: 0.7204 (p) REVERT: T 59 MET cc_start: 0.8518 (tpp) cc_final: 0.8204 (tpp) REVERT: T 70 PHE cc_start: 0.9086 (t80) cc_final: 0.8618 (t80) REVERT: T 71 GLU cc_start: 0.9416 (mm-30) cc_final: 0.8946 (mm-30) REVERT: T 79 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.7952 (ptm-80) REVERT: T 95 GLN cc_start: 0.8801 (tt0) cc_final: 0.8450 (tp40) REVERT: T 99 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8255 (mtt-85) REVERT: T 113 GLU cc_start: 0.8339 (tt0) cc_final: 0.7515 (pp20) outliers start: 113 outliers final: 89 residues processed: 560 average time/residue: 0.2675 time to fit residues: 249.5402 Evaluate side-chains 572 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 471 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 359 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 398 SER Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 593 PHE Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 1044 LEU Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1126 MET Chi-restraints excluded: chain G residue 1137 MET Chi-restraints excluded: chain G residue 1235 LEU Chi-restraints excluded: chain G residue 1245 GLN Chi-restraints excluded: chain H residue 234 HIS Chi-restraints excluded: chain I residue 124 PHE Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 233 HIS Chi-restraints excluded: chain J residue 252 ILE Chi-restraints excluded: chain J residue 444 VAL Chi-restraints excluded: chain J residue 468 ILE Chi-restraints excluded: chain J residue 481 LYS Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 577 ILE Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 25 PHE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain S residue 19 SER Chi-restraints excluded: chain S residue 38 ASN Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 93 optimal weight: 0.2980 chunk 245 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 249 optimal weight: 4.9990 chunk 294 optimal weight: 0.8980 chunk 327 optimal weight: 30.0000 chunk 68 optimal weight: 0.0980 chunk 261 optimal weight: 5.9990 chunk 31 optimal weight: 0.2980 chunk 227 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 GLN M 85 GLN M 108 ASN N 25 ASN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 HIS ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** 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 = 0.3916 r_free = 0.3916 target = 0.113218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.073852 restraints weight = 108373.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.076770 restraints weight = 47415.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.076910 restraints weight = 22788.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.077387 restraints weight = 19160.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.077459 restraints weight = 18515.443| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 44424 Z= 0.133 Angle : 0.668 13.876 61158 Z= 0.351 Chirality : 0.045 0.320 6942 Planarity : 0.004 0.100 6851 Dihedral : 21.764 167.991 8316 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.80 % Favored : 97.09 % Rotamer: Outliers : 2.43 % Allowed : 17.67 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.22 (0.12), residues: 4675 helix: 0.53 (0.11), residues: 2222 sheet: -0.87 (0.20), residues: 576 loop : -0.58 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG F 213 TYR 0.038 0.002 TYR N 88 PHE 0.022 0.001 PHE N 100 TRP 0.022 0.001 TRP G1061 HIS 0.006 0.001 HIS O 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (44424) covalent geometry : angle 0.66789 / 0.35 (61158) hydrogen bonds : bond 0.03954 / 2.55 ( 1957) hydrogen bonds : angle 4.30783 / 3.01 ( 5316) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 506 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8845 (mmm) cc_final: 0.7903 (mmm) REVERT: A 211 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8486 (p) REVERT: A 320 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: A 346 SER cc_start: 0.9276 (t) cc_final: 0.8929 (p) REVERT: B 186 GLU cc_start: 0.7118 (pp20) cc_final: 0.6609 (pp20) REVERT: B 278 GLU cc_start: 0.7820 (tp30) cc_final: 0.7167 (tp30) REVERT: B 356 ASP cc_start: 0.8520 (m-30) cc_final: 0.8286 (m-30) REVERT: C 273 ASP cc_start: 0.8426 (t0) cc_final: 0.8098 (t0) REVERT: C 306 MET cc_start: 0.8596 (mmm) cc_final: 0.8322 (mmm) REVERT: C 371 MET cc_start: 0.8807 (tpp) cc_final: 0.8190 (mmt) REVERT: D 35 ASP cc_start: 0.8324 (m-30) cc_final: 0.8029 (t0) REVERT: D 248 ASP cc_start: 0.7988 (m-30) cc_final: 0.7781 (m-30) REVERT: D 282 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7835 (tm-30) REVERT: E 149 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6152 (tmm-80) REVERT: E 178 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8050 (tmm) REVERT: E 197 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8413 (mtpt) REVERT: E 264 ASP cc_start: 0.8046 (t0) cc_final: 0.7356 (t0) REVERT: F 162 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8189 (p) REVERT: G 739 LEU cc_start: 0.7946 (tp) cc_final: 0.7508 (mm) REVERT: G 929 LEU cc_start: 0.9088 (tt) cc_final: 0.8779 (mt) REVERT: G 1048 GLN cc_start: 0.8454 (mt0) cc_final: 0.7688 (mp10) REVERT: G 1126 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.7734 (mtm) REVERT: G 1148 ASP cc_start: 0.8248 (t0) cc_final: 0.7582 (p0) REVERT: H 215 LYS cc_start: 0.6836 (tttp) cc_final: 0.6408 (mmtt) REVERT: H 224 ARG cc_start: 0.8088 (tpp-160) cc_final: 0.7680 (tpp-160) REVERT: H 272 MET cc_start: 0.8618 (mmm) cc_final: 0.8074 (mmp) REVERT: I 145 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8419 (pttm) REVERT: I 187 ASN cc_start: 0.8741 (m-40) cc_final: 0.8514 (m110) REVERT: J 107 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6605 (pt0) REVERT: J 148 MET cc_start: 0.9003 (tpp) cc_final: 0.8757 (tpp) REVERT: J 481 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8496 (tptt) REVERT: M 94 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8163 (tp30) REVERT: N 30 THR cc_start: 0.8881 (p) cc_final: 0.8660 (t) REVERT: N 68 ASP cc_start: 0.8379 (m-30) cc_final: 0.8008 (t0) REVERT: N 84 MET cc_start: 0.8470 (mmp) cc_final: 0.8219 (tmm) REVERT: N 88 TYR cc_start: 0.8445 (m-10) cc_final: 0.7985 (m-80) REVERT: N 98 TYR cc_start: 0.7611 (m-10) cc_final: 0.7324 (m-80) REVERT: O 42 ARG cc_start: 0.8233 (mtp-110) cc_final: 0.8024 (mtp-110) REVERT: O 56 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8714 (mm-30) REVERT: O 63 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8506 (pp) REVERT: O 91 GLU cc_start: 0.9003 (pm20) cc_final: 0.8344 (pp20) REVERT: O 92 GLU cc_start: 0.7873 (mt-10) cc_final: 0.6300 (tt0) REVERT: O 102 ILE cc_start: 0.7840 (mp) cc_final: 0.7629 (mm) REVERT: P 59 MET cc_start: 0.8589 (mmm) cc_final: 0.8343 (mmm) REVERT: P 62 MET cc_start: 0.9236 (tpp) cc_final: 0.8723 (tpp) REVERT: P 105 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8089 (pm20) REVERT: Q 90 MET cc_start: 0.7835 (mmp) cc_final: 0.7402 (mtt) REVERT: Q 122 LYS cc_start: 0.8614 (pttm) cc_final: 0.7800 (tppt) REVERT: Q 134 ARG cc_start: 0.7826 (mtt180) cc_final: 0.7511 (ptm160) REVERT: R 35 ARG cc_start: 0.8198 (mmm-85) cc_final: 0.7976 (tpp80) REVERT: R 50 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7696 (mm) REVERT: R 93 GLN cc_start: 0.8563 (mt0) cc_final: 0.8300 (mt0) REVERT: S 100 VAL cc_start: 0.7438 (p) cc_final: 0.7169 (p) REVERT: T 59 MET cc_start: 0.8488 (tpp) cc_final: 0.8201 (tpp) REVERT: T 70 PHE cc_start: 0.9087 (t80) cc_final: 0.8792 (t80) REVERT: T 71 GLU cc_start: 0.9434 (mm-30) cc_final: 0.9060 (mm-30) REVERT: T 95 GLN cc_start: 0.8772 (tt0) cc_final: 0.8405 (tp40) REVERT: T 99 ARG cc_start: 0.8601 (tpp80) cc_final: 0.8275 (mtt-85) REVERT: T 113 GLU cc_start: 0.8339 (tt0) cc_final: 0.7543 (pp20) outliers start: 98 outliers final: 74 residues processed: 569 average time/residue: 0.2765 time to fit residues: 260.5809 Evaluate side-chains 560 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 476 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 359 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 398 SER Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 593 PHE Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 1044 LEU Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1126 MET Chi-restraints excluded: chain G residue 1137 MET Chi-restraints excluded: chain G residue 1235 LEU Chi-restraints excluded: chain G residue 1245 GLN Chi-restraints excluded: chain I residue 124 PHE Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 233 HIS Chi-restraints excluded: chain J residue 444 VAL Chi-restraints excluded: chain J residue 481 LYS Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 577 ILE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain O residue 25 PHE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 105 GLU Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain S residue 19 SER Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 38 ASN Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 196 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 chunk 233 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 280 optimal weight: 9.9990 chunk 222 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 296 optimal weight: 0.6980 chunk 452 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 ASN E 344 HIS ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 675 ASN ** G1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN N 25 ASN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.113009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.074265 restraints weight = 106359.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.076586 restraints weight = 46229.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.076998 restraints weight = 24536.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.077646 restraints weight = 18856.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.077651 restraints weight = 16985.564| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 44424 Z= 0.142 Angle : 0.663 13.768 61158 Z= 0.349 Chirality : 0.045 0.309 6942 Planarity : 0.004 0.060 6851 Dihedral : 21.731 168.276 8316 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.04 % Favored : 96.88 % Rotamer: Outliers : 2.41 % Allowed : 17.87 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.17 (0.12), residues: 4675 helix: 0.58 (0.11), residues: 2227 sheet: -0.84 (0.20), residues: 576 loop : -0.58 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG R 67 TYR 0.039 0.001 TYR N 88 PHE 0.022 0.001 PHE M 67 TRP 0.020 0.001 TRP G1061 HIS 0.006 0.001 HIS O 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (44424) covalent geometry : angle 0.66349 / 0.35 (61158) hydrogen bonds : bond 0.03922 / 2.52 ( 1957) hydrogen bonds : angle 4.28906 / 3.00 ( 5316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9414.90 seconds wall clock time: 162 minutes 48.98 seconds (9768.98 seconds total)