Starting phenix.real_space_refine on Sun Feb 8 09:13:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gfb_51312/02_2026/9gfb_51312.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gfb_51312/02_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_51312/02_2026/9gfb_51312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gfb_51312/02_2026/9gfb_51312.map" model { file = "/net/cci-nas-00/data/ceres_data/9gfb_51312/02_2026/9gfb_51312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gfb_51312/02_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 9.69, 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: 2.91 Conformation dependent library (CDL) restraints added in 1.4 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: 5.66 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: 11.68 Time building geometry restraints manager: 3.86 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: 58859 3.94 - 7.87: 2254 7.87 - 11.81: 31 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=" CA ASP D 248 " pdb=" CB ASP D 248 " pdb=" CG ASP D 248 " ideal model delta sigma weight residual 112.60 121.57 -8.97 1.00e+00 1.00e+00 8.05e+01 angle pdb=" CA PRO M 43 " pdb=" N PRO M 43 " pdb=" CD PRO M 43 " ideal model delta sigma weight residual 112.00 101.71 10.29 1.40e+00 5.10e-01 5.40e+01 angle pdb=" N SER G 574 " pdb=" CA SER G 574 " pdb=" C SER G 574 " ideal model delta sigma weight residual 108.22 114.24 -6.02 9.00e-01 1.23e+00 4.48e+01 ... (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 - 0.098: 5018 0.098 - 0.196: 1682 0.196 - 0.293: 206 0.293 - 0.391: 27 0.391 - 0.489: 9 Chirality restraints: 6942 Sorted by residual: 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 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 -2.66 -2.21 -0.45 2.00e-01 2.50e+01 5.03e+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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 43.300 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 0.012 0.149 44424 Z= 0.736 Angle : 1.861 19.684 61158 Z= 1.226 Chirality : 0.092 0.489 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 covalent geometry : bond 0.01242 (44424) covalent geometry : angle 1.86124 (61158) hydrogen bonds : bond 0.15708 ( 1957) hydrogen bonds : angle 7.40651 ( 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 : 1.903 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: 0.8360 (p) REVERT: E 313 ASN cc_start: 0.8658 (m-40) cc_final: 0.7945 (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: 0.5268 (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: 0.8747 (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: 0.8216 (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: M 118 THR cc_start: 0.6702 (m) cc_final: 0.6464 (p) REVERT: N 35 ARG cc_start: 0.9159 (mtt180) cc_final: 0.8926 (mmm160) REVERT: N 90 LEU cc_start: 0.9050 (mt) cc_final: 0.8835 (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 107 THR cc_start: 0.8860 (m) cc_final: 0.8611 (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: 0.6872 (p) REVERT: T 46 LYS cc_start: 0.8748 (mmtm) cc_final: 0.8547 (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: 0.8322 (tp40) REVERT: T 96 THR cc_start: 0.8553 (m) cc_final: 0.8316 (p) REVERT: T 109 HIS cc_start: 0.8490 (m-70) cc_final: 0.7830 (m90) outliers start: 35 outliers final: 10 residues processed: 936 average time/residue: 0.3139 time to fit residues: 463.3747 Evaluate side-chains 566 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 555 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 348 HIS C 408 GLN D 78 GLN D 92 GLN D 146 GLN E 255 GLN ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 672 GLN G 989 HIS G1164 GLN H 150 GLN ** H 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 236 ASN I 126 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 ASN ** 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 S 110 ASN T 109 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.113832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.073874 restraints weight = 108952.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.076026 restraints weight = 47793.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.077418 restraints weight = 27508.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.078300 restraints weight = 19032.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.078854 restraints weight = 14977.170| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 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 = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 44424 Z= 0.193 Angle : 0.747 8.836 61158 Z= 0.406 Chirality : 0.046 0.236 6942 Planarity : 0.005 0.044 6851 Dihedral : 21.584 165.935 8327 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.84 % Favored : 97.03 % Rotamer: Outliers : 2.58 % Allowed : 10.99 % Favored : 86.43 % 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: -0.77 (0.12), residues: 4675 helix: -0.26 (0.11), residues: 2211 sheet: -0.52 (0.20), residues: 601 loop : -0.60 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 11 TYR 0.020 0.002 TYR Q 99 PHE 0.024 0.002 PHE G 853 TRP 0.025 0.002 TRP J 540 HIS 0.010 0.001 HIS J 130 Details of bonding type rmsd covalent geometry : bond 0.00394 (44424) covalent geometry : angle 0.74705 (61158) hydrogen bonds : bond 0.05152 ( 1957) hydrogen bonds : angle 4.78287 ( 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 750 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 646 time to evaluate : 1.611 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: A 99 SER cc_start: 0.8782 (t) cc_final: 0.8517 (t) REVERT: A 211 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8807 (p) REVERT: A 346 SER cc_start: 0.9322 (t) cc_final: 0.9055 (p) REVERT: B 113 MET cc_start: 0.8799 (mmm) cc_final: 0.8562 (tpp) REVERT: C 113 MET cc_start: 0.8354 (tpt) cc_final: 0.8021 (tpt) REVERT: C 278 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8195 (mm-30) REVERT: C 408 GLN cc_start: 0.8733 (tt0) cc_final: 0.8480 (mt0) REVERT: D 35 ASP cc_start: 0.8414 (m-30) cc_final: 0.8119 (t70) REVERT: E 178 MET cc_start: 0.8601 (tmm) cc_final: 0.8016 (tmm) REVERT: E 201 LYS cc_start: 0.9137 (mttp) cc_final: 0.8866 (mtmm) REVERT: E 246 GLU cc_start: 0.7854 (pt0) cc_final: 0.7474 (pt0) REVERT: E 264 ASP cc_start: 0.7902 (t0) cc_final: 0.7037 (t0) REVERT: F 46 MET cc_start: 0.8039 (mtp) cc_final: 0.7816 (mtp) REVERT: F 144 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: F 291 ILE cc_start: 0.9228 (mt) cc_final: 0.8969 (tt) REVERT: G 649 MET cc_start: 0.7734 (ptm) cc_final: 0.7239 (ptp) REVERT: G 929 LEU cc_start: 0.9101 (tt) cc_final: 0.8865 (mt) REVERT: G 1048 GLN cc_start: 0.8584 (mt0) cc_final: 0.8280 (mt0) REVERT: G 1134 GLU cc_start: 0.8895 (tt0) cc_final: 0.8572 (mt-10) REVERT: G 1136 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.8215 (t80) REVERT: H 215 LYS cc_start: 0.5975 (tttp) cc_final: 0.5451 (mmtt) REVERT: H 224 ARG cc_start: 0.7710 (tpp-160) cc_final: 0.7471 (tpp-160) REVERT: H 272 MET cc_start: 0.8490 (mmm) cc_final: 0.8035 (mmp) REVERT: I 143 ASN cc_start: 0.7472 (m-40) cc_final: 0.6918 (m-40) REVERT: I 148 LEU cc_start: 0.8882 (mm) cc_final: 0.8486 (mm) REVERT: I 194 LYS cc_start: 0.9014 (mttt) cc_final: 0.8645 (mmmt) REVERT: J 48 CYS cc_start: 0.8638 (t) cc_final: 0.8271 (p) REVERT: J 110 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: J 114 ASP cc_start: 0.7873 (m-30) cc_final: 0.7241 (m-30) REVERT: M 94 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8274 (tp30) REVERT: M 122 LYS cc_start: 0.7904 (tptt) cc_final: 0.7623 (tttt) REVERT: N 58 LEU cc_start: 0.9255 (tp) cc_final: 0.8970 (pp) REVERT: N 84 MET cc_start: 0.8639 (mmp) cc_final: 0.8237 (tmm) REVERT: N 88 TYR cc_start: 0.8328 (m-10) cc_final: 0.7962 (m-10) REVERT: O 33 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7973 (pp) REVERT: O 54 VAL cc_start: 0.9418 (t) cc_final: 0.9183 (m) REVERT: O 84 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7832 (mm110) REVERT: O 91 GLU cc_start: 0.8936 (pm20) cc_final: 0.8540 (pp20) REVERT: O 92 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7823 (mt-10) REVERT: O 104 GLN cc_start: 0.8566 (pt0) cc_final: 0.8328 (pt0) REVERT: P 37 TYR cc_start: 0.8354 (m-10) cc_final: 0.8135 (m-10) REVERT: P 62 MET cc_start: 0.9478 (mmm) cc_final: 0.9181 (tpp) REVERT: P 67 ASN cc_start: 0.8229 (p0) cc_final: 0.7405 (p0) REVERT: P 76 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8740 (mm-30) REVERT: P 115 THR cc_start: 0.8522 (m) cc_final: 0.8276 (p) REVERT: Q 90 MET cc_start: 0.8009 (mmp) cc_final: 0.7489 (mtt) REVERT: Q 134 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7318 (ptm160) REVERT: R 35 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7946 (mtp180) REVERT: R 63 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7795 (tm-30) REVERT: R 72 TYR cc_start: 0.8987 (m-80) cc_final: 0.8668 (m-80) REVERT: S 56 GLU cc_start: 0.7722 (tt0) cc_final: 0.7514 (mt-10) REVERT: S 57 TYR cc_start: 0.8399 (t80) cc_final: 0.7862 (t80) REVERT: S 94 ASN cc_start: 0.8400 (t0) cc_final: 0.7886 (m110) REVERT: S 100 VAL cc_start: 0.7304 (p) cc_final: 0.6227 (p) REVERT: S 104 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7770 (tm-30) REVERT: T 37 TYR cc_start: 0.8604 (m-80) cc_final: 0.8390 (m-80) REVERT: T 49 HIS cc_start: 0.7430 (m-70) cc_final: 0.7129 (m-70) REVERT: T 59 MET cc_start: 0.8899 (tpp) cc_final: 0.8601 (tpp) REVERT: T 70 PHE cc_start: 0.9158 (t80) cc_final: 0.8695 (t80) REVERT: T 71 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8919 (mm-30) REVERT: T 79 ARG cc_start: 0.8390 (ttp-110) cc_final: 0.7895 (ptm-80) REVERT: T 95 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8320 (tp40) REVERT: T 96 THR cc_start: 0.8439 (m) cc_final: 0.8181 (p) REVERT: T 109 HIS cc_start: 0.7855 (m90) cc_final: 0.7385 (m90) REVERT: T 113 GLU cc_start: 0.8452 (tt0) cc_final: 0.7656 (pp20) outliers start: 104 outliers final: 48 residues processed: 710 average time/residue: 0.2893 time to fit residues: 333.9837 Evaluate side-chains 572 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 517 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 211 THR 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 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 D residue 429 VAL 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 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 769 SER 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 296 VAL Chi-restraints excluded: chain I residue 124 PHE Chi-restraints excluded: chain J residue 110 GLU 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 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 67 PHE Chi-restraints excluded: chain Q residue 124 ILE 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 T residue 45 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 95 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 262 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 479 optimal weight: 8.9990 chunk 369 optimal weight: 3.9990 chunk 250 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 343 optimal weight: 30.0000 chunk 152 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 456 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN D 146 GLN D 422 GLN E 146 GLN ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 302 HIS ** 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** J 130 HIS ** J 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN N 25 ASN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.112127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.071903 restraints weight = 108759.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.073997 restraints weight = 48042.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.075347 restraints weight = 27992.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.076227 restraints weight = 19531.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.076770 restraints weight = 15421.272| |-----------------------------------------------------------------------------| 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 = 0.44 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 44424 Z= 0.195 Angle : 0.687 9.862 61158 Z= 0.370 Chirality : 0.045 0.226 6942 Planarity : 0.004 0.051 6851 Dihedral : 21.639 165.838 8321 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.36 % Favored : 96.53 % Rotamer: Outliers : 3.00 % Allowed : 13.13 % Favored : 83.87 % 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: -0.53 (0.12), residues: 4675 helix: 0.07 (0.11), residues: 2211 sheet: -0.64 (0.20), residues: 610 loop : -0.58 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 213 TYR 0.027 0.002 TYR N 72 PHE 0.024 0.002 PHE M 67 TRP 0.020 0.002 TRP G1061 HIS 0.008 0.001 HIS O 31 Details of bonding type rmsd covalent geometry : bond 0.00446 (44424) covalent geometry : angle 0.68718 (61158) hydrogen bonds : bond 0.04596 ( 1957) hydrogen bonds : angle 4.56990 ( 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 683 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 562 time to evaluate : 1.680 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: 0.8796 (t) cc_final: 0.8547 (t) REVERT: A 178 GLU cc_start: 0.8874 (tt0) cc_final: 0.8670 (mt-10) REVERT: A 346 SER cc_start: 0.9352 (t) cc_final: 0.9063 (p) REVERT: B 114 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8134 (mt-10) REVERT: C 61 MET cc_start: 0.8363 (mmm) cc_final: 0.8079 (mmm) REVERT: C 113 MET cc_start: 0.8401 (tpt) cc_final: 0.8070 (tpt) REVERT: C 181 GLN cc_start: 0.8552 (pt0) cc_final: 0.8276 (pp30) REVERT: D 35 ASP cc_start: 0.8327 (m-30) cc_final: 0.7985 (t0) REVERT: D 313 ASN cc_start: 0.8775 (m-40) cc_final: 0.8095 (t0) REVERT: E 178 MET cc_start: 0.8522 (tmm) cc_final: 0.7973 (tmm) REVERT: E 201 LYS cc_start: 0.9156 (mttp) cc_final: 0.8928 (mtmm) REVERT: E 246 GLU cc_start: 0.7847 (pt0) cc_final: 0.7419 (pt0) REVERT: F 144 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: F 162 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8275 (p) REVERT: F 291 ILE cc_start: 0.9292 (mt) cc_final: 0.9051 (tt) REVERT: G 668 LEU cc_start: 0.9055 (mt) cc_final: 0.8800 (mm) REVERT: G 688 MET cc_start: 0.8690 (mmp) cc_final: 0.8467 (mtt) REVERT: G 929 LEU cc_start: 0.9135 (tt) cc_final: 0.8826 (mt) REVERT: H 215 LYS cc_start: 0.6099 (tttp) cc_final: 0.5623 (mmtt) REVERT: H 272 MET cc_start: 0.8462 (mmm) cc_final: 0.7799 (mmp) REVERT: I 143 ASN cc_start: 0.8057 (m-40) cc_final: 0.7539 (m-40) REVERT: I 148 LEU cc_start: 0.8675 (mm) cc_final: 0.8308 (mm) REVERT: I 152 ARG cc_start: 0.7435 (tpp80) cc_final: 0.6755 (mpt-90) REVERT: J 48 CYS cc_start: 0.8631 (t) cc_final: 0.8310 (p) REVERT: M 94 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8238 (tp30) REVERT: N 44 LYS cc_start: 0.8301 (mtmt) cc_final: 0.8038 (mtmm) REVERT: N 58 LEU cc_start: 0.9272 (tp) cc_final: 0.9011 (pp) REVERT: N 63 GLU cc_start: 0.9129 (pt0) cc_final: 0.8846 (pp20) REVERT: N 64 ASN cc_start: 0.8503 (p0) cc_final: 0.8047 (p0) REVERT: N 84 MET cc_start: 0.8595 (mmp) cc_final: 0.8218 (tmm) REVERT: N 88 TYR cc_start: 0.8312 (m-10) cc_final: 0.7843 (m-10) REVERT: N 91 LYS cc_start: 0.9348 (mmmt) cc_final: 0.9054 (mmmm) REVERT: N 98 TYR cc_start: 0.8194 (m-10) cc_final: 0.7693 (m-10) REVERT: O 33 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8044 (pp) REVERT: O 91 GLU cc_start: 0.8927 (pm20) cc_final: 0.8364 (pp20) REVERT: O 99 ARG cc_start: 0.7445 (mmm-85) cc_final: 0.7007 (tmm-80) REVERT: P 59 MET cc_start: 0.8676 (tpt) cc_final: 0.8370 (mmm) REVERT: P 62 MET cc_start: 0.9418 (mmm) cc_final: 0.9042 (tpp) REVERT: P 70 PHE cc_start: 0.8679 (t80) cc_final: 0.8455 (t80) REVERT: Q 61 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6991 (mt) REVERT: Q 90 MET cc_start: 0.7952 (mmp) cc_final: 0.7637 (mtt) REVERT: Q 134 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7360 (ptm160) REVERT: R 44 LYS cc_start: 0.8167 (pptt) cc_final: 0.7864 (pptt) REVERT: R 63 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7825 (tm-30) REVERT: R 72 TYR cc_start: 0.9085 (m-80) cc_final: 0.8770 (m-80) REVERT: R 91 LYS cc_start: 0.9151 (tptt) cc_final: 0.8792 (tptt) REVERT: S 64 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8748 (tm-30) REVERT: S 94 ASN cc_start: 0.8393 (t0) cc_final: 0.7811 (m110) REVERT: T 59 MET cc_start: 0.8741 (tpp) cc_final: 0.8394 (tpp) REVERT: T 70 PHE cc_start: 0.9203 (t80) cc_final: 0.8745 (t80) REVERT: T 71 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8952 (mm-30) REVERT: T 79 ARG cc_start: 0.8338 (ttp-110) cc_final: 0.7888 (ptm-80) REVERT: T 95 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8488 (tp40) REVERT: T 113 GLU cc_start: 0.8505 (tt0) cc_final: 0.7641 (pp20) outliers start: 121 outliers final: 65 residues processed: 648 average time/residue: 0.2643 time to fit residues: 282.1738 Evaluate side-chains 565 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 495 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 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 260 MET 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 343 ASP 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 199 THR 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 426 ILE 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 413 CYS 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 162 THR Chi-restraints excluded: chain F residue 174 LEU 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 821 LEU Chi-restraints excluded: chain G residue 1044 LEU 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 J residue 110 GLU Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 577 ILE Chi-restraints excluded: chain M residue 56 LYS Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 92 ARG Chi-restraints excluded: chain O residue 33 LEU 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 61 LEU Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 68 ASP 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 110 ASN Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 95 GLN Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 228 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 263 optimal weight: 1.9990 chunk 329 optimal weight: 40.0000 chunk 336 optimal weight: 0.7980 chunk 167 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 310 optimal weight: 0.0010 chunk 81 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 241 HIS D 302 HIS ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 HIS 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 J 440 HIS N 25 ASN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 GLN ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.113252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.073175 restraints weight = 108771.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.075261 restraints weight = 47761.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.076672 restraints weight = 27736.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.077551 restraints weight = 19252.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.078081 restraints weight = 15221.563| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 44424 Z= 0.149 Angle : 0.642 8.915 61158 Z= 0.344 Chirality : 0.043 0.243 6942 Planarity : 0.004 0.067 6851 Dihedral : 21.588 164.591 8320 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.93 % Favored : 96.98 % Rotamer: Outliers : 2.85 % Allowed : 13.80 % Favored : 83.35 % 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: -0.34 (0.12), residues: 4675 helix: 0.29 (0.11), residues: 2220 sheet: -0.59 (0.20), residues: 579 loop : -0.56 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 213 TYR 0.027 0.002 TYR J 564 PHE 0.021 0.001 PHE M 67 TRP 0.022 0.001 TRP G1061 HIS 0.012 0.001 HIS O 31 Details of bonding type rmsd covalent geometry : bond 0.00334 (44424) covalent geometry : angle 0.64207 (61158) hydrogen bonds : bond 0.04090 ( 1957) hydrogen bonds : angle 4.37617 ( 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 670 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 555 time to evaluate : 1.449 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: A 99 SER cc_start: 0.8631 (t) cc_final: 0.8390 (t) REVERT: A 211 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8759 (p) REVERT: A 346 SER cc_start: 0.9307 (t) cc_final: 0.9015 (p) REVERT: B 114 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8101 (mt-10) REVERT: B 218 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6951 (mm-30) REVERT: B 314 TYR cc_start: 0.8816 (t80) cc_final: 0.8598 (t80) REVERT: B 415 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8843 (mt) REVERT: C 113 MET cc_start: 0.8273 (tpt) cc_final: 0.8017 (tpt) REVERT: C 181 GLN cc_start: 0.8501 (pt0) cc_final: 0.8184 (pp30) REVERT: D 35 ASP cc_start: 0.8345 (m-30) cc_final: 0.8010 (t0) REVERT: D 147 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8148 (mm) REVERT: D 349 ASP cc_start: 0.7525 (t0) cc_final: 0.6891 (t0) REVERT: E 178 MET cc_start: 0.8513 (tmm) cc_final: 0.7925 (tmm) REVERT: E 197 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8352 (mtpt) REVERT: E 201 LYS cc_start: 0.9184 (mttp) cc_final: 0.8930 (mtmm) REVERT: F 162 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8189 (p) REVERT: F 291 ILE cc_start: 0.9253 (mt) cc_final: 0.9016 (tt) REVERT: F 382 MET cc_start: 0.7681 (mtp) cc_final: 0.7245 (mtp) REVERT: G 649 MET cc_start: 0.7890 (ptm) cc_final: 0.7394 (ppp) REVERT: G 929 LEU cc_start: 0.9129 (tt) cc_final: 0.8842 (mt) REVERT: G 1145 MET cc_start: 0.7625 (mmm) cc_final: 0.7342 (mmt) REVERT: G 1148 ASP cc_start: 0.8276 (t0) cc_final: 0.7515 (p0) REVERT: H 215 LYS cc_start: 0.6334 (tttp) cc_final: 0.5870 (mmtt) REVERT: H 224 ARG cc_start: 0.7735 (tpp-160) cc_final: 0.7465 (tpp-160) REVERT: H 272 MET cc_start: 0.8486 (mmm) cc_final: 0.8050 (mmp) REVERT: I 143 ASN cc_start: 0.8211 (m-40) cc_final: 0.7619 (m-40) REVERT: I 152 ARG cc_start: 0.7516 (tpp80) cc_final: 0.7160 (tpp80) REVERT: I 194 LYS cc_start: 0.8913 (mttt) cc_final: 0.8709 (mmmt) REVERT: J 48 CYS cc_start: 0.8614 (t) cc_final: 0.8289 (p) REVERT: J 486 MET cc_start: 0.8464 (tmm) cc_final: 0.8250 (tmm) REVERT: J 565 LEU cc_start: 0.7775 (tp) cc_final: 0.7358 (pp) REVERT: M 67 PHE cc_start: 0.9242 (t80) cc_final: 0.8673 (t80) REVERT: M 94 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8336 (tp30) REVERT: N 84 MET cc_start: 0.8583 (mmp) cc_final: 0.8235 (tmm) REVERT: N 88 TYR cc_start: 0.8366 (m-10) cc_final: 0.7842 (m-10) REVERT: N 91 LYS cc_start: 0.9347 (mmmt) cc_final: 0.9094 (mmmm) REVERT: N 98 TYR cc_start: 0.8075 (m-10) cc_final: 0.7664 (m-80) REVERT: O 33 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8026 (pp) REVERT: O 91 GLU cc_start: 0.8931 (pm20) cc_final: 0.8446 (pp20) REVERT: O 102 ILE cc_start: 0.8004 (mp) cc_final: 0.7763 (mm) REVERT: P 42 TYR cc_start: 0.8115 (t80) cc_final: 0.7896 (t80) REVERT: P 59 MET cc_start: 0.8753 (tpt) cc_final: 0.8487 (mmm) REVERT: P 62 MET cc_start: 0.9443 (mmm) cc_final: 0.9221 (tpp) REVERT: Q 90 MET cc_start: 0.7954 (mmp) cc_final: 0.7601 (mtt) REVERT: Q 134 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7358 (ptm160) REVERT: R 44 LYS cc_start: 0.8172 (pptt) cc_final: 0.7897 (pptt) REVERT: R 63 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7747 (tm-30) REVERT: R 72 TYR cc_start: 0.9110 (m-80) cc_final: 0.8777 (m-80) REVERT: T 39 ILE cc_start: 0.8543 (pt) cc_final: 0.8218 (pt) REVERT: T 59 MET cc_start: 0.8686 (tpp) cc_final: 0.8352 (tpp) REVERT: T 70 PHE cc_start: 0.9217 (t80) cc_final: 0.8773 (t80) REVERT: T 71 GLU cc_start: 0.9408 (mm-30) cc_final: 0.8978 (mm-30) REVERT: T 79 ARG cc_start: 0.8318 (ttp-110) cc_final: 0.7905 (ptm-80) REVERT: T 95 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8514 (tp40) REVERT: T 113 GLU cc_start: 0.8523 (tt0) cc_final: 0.7695 (pp20) outliers start: 115 outliers final: 54 residues processed: 634 average time/residue: 0.2569 time to fit residues: 268.9805 Evaluate side-chains 537 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 477 time to evaluate : 1.607 ------------------------------------------------------------------------------- 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 B residue 19 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 415 LEU 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 147 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 199 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 426 ILE 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 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 1078 SER Chi-restraints excluded: chain G residue 1235 LEU Chi-restraints excluded: chain I residue 124 PHE Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 110 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 M residue 46 VAL Chi-restraints excluded: chain M residue 56 LYS Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 68 ASP 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 95 GLN Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 330 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 166 optimal weight: 0.0370 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 323 optimal weight: 3.9990 chunk 384 optimal weight: 3.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN C 373 GLN E 344 HIS ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** H 298 GLN M 108 ASN N 25 ASN ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** 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 = 0.3918 r_free = 0.3918 target = 0.113240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.073509 restraints weight = 108571.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.076312 restraints weight = 49627.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.076833 restraints weight = 25257.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.077105 restraints weight = 18576.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.077491 restraints weight = 17672.853| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 44424 Z= 0.142 Angle : 0.625 10.157 61158 Z= 0.333 Chirality : 0.042 0.202 6942 Planarity : 0.004 0.061 6851 Dihedral : 21.518 163.767 8319 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.84 % Favored : 97.05 % Rotamer: Outliers : 3.05 % Allowed : 14.76 % Favored : 82.18 % 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: -0.21 (0.12), residues: 4675 helix: 0.43 (0.11), residues: 2219 sheet: -0.64 (0.20), residues: 564 loop : -0.51 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 213 TYR 0.027 0.001 TYR S 57 PHE 0.029 0.001 PHE M 67 TRP 0.022 0.001 TRP G1061 HIS 0.005 0.001 HIS F 27 Details of bonding type rmsd covalent geometry : bond 0.00318 (44424) covalent geometry : angle 0.62521 (61158) hydrogen bonds : bond 0.03842 ( 1957) hydrogen bonds : angle 4.27316 ( 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 673 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 550 time to evaluate : 1.356 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: A 61 MET cc_start: 0.8824 (mmm) cc_final: 0.7749 (mmm) REVERT: A 99 SER cc_start: 0.8587 (t) cc_final: 0.8366 (t) REVERT: A 211 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8752 (p) REVERT: A 320 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7575 (mm-30) REVERT: A 346 SER cc_start: 0.9284 (t) cc_final: 0.8959 (p) REVERT: B 114 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8113 (mt-10) REVERT: B 161 LEU cc_start: 0.8482 (mt) cc_final: 0.8267 (mt) REVERT: C 61 MET cc_start: 0.8221 (mmm) cc_final: 0.7990 (mmm) REVERT: C 113 MET cc_start: 0.8264 (tpt) cc_final: 0.8063 (tpt) REVERT: D 35 ASP cc_start: 0.8390 (m-30) cc_final: 0.8091 (t0) REVERT: D 147 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7962 (mm) REVERT: E 149 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6311 (tmm-80) REVERT: E 201 LYS cc_start: 0.9208 (mttp) cc_final: 0.8945 (mtmm) REVERT: F 46 MET cc_start: 0.8138 (mtp) cc_final: 0.7805 (mtp) REVERT: F 162 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8184 (p) REVERT: F 291 ILE cc_start: 0.9226 (mt) cc_final: 0.9004 (tt) REVERT: G 649 MET cc_start: 0.7850 (ptm) cc_final: 0.7370 (ppp) REVERT: G 668 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8454 (mp) REVERT: G 688 MET cc_start: 0.8685 (mmp) cc_final: 0.8418 (mtt) REVERT: G 929 LEU cc_start: 0.9115 (tt) cc_final: 0.8831 (mt) REVERT: G 1145 MET cc_start: 0.7569 (mmm) cc_final: 0.7348 (mmt) REVERT: G 1148 ASP cc_start: 0.8247 (t0) cc_final: 0.7545 (p0) REVERT: H 215 LYS cc_start: 0.6475 (tttp) cc_final: 0.5967 (mmtt) REVERT: H 224 ARG cc_start: 0.7923 (tpp-160) cc_final: 0.7588 (tpp-160) REVERT: H 272 MET cc_start: 0.8550 (mmm) cc_final: 0.8030 (mmp) REVERT: I 145 LYS cc_start: 0.8977 (ttmm) cc_final: 0.8736 (pttm) REVERT: I 152 ARG cc_start: 0.7624 (tpp80) cc_final: 0.7144 (tpp80) REVERT: J 48 CYS cc_start: 0.8647 (t) cc_final: 0.8238 (p) REVERT: J 148 MET cc_start: 0.9053 (tpp) cc_final: 0.8827 (tpp) REVERT: J 481 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8489 (tptt) REVERT: J 486 MET cc_start: 0.8512 (tmm) cc_final: 0.8272 (tmm) REVERT: M 94 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8482 (tp30) REVERT: N 58 LEU cc_start: 0.9263 (tp) cc_final: 0.8969 (pp) REVERT: N 68 ASP cc_start: 0.8449 (m-30) cc_final: 0.7920 (t0) REVERT: N 72 TYR cc_start: 0.6997 (m-80) cc_final: 0.5841 (m-80) REVERT: N 84 MET cc_start: 0.8541 (mmp) cc_final: 0.8253 (tmm) REVERT: N 88 TYR cc_start: 0.8324 (m-10) cc_final: 0.7976 (m-10) REVERT: N 91 LYS cc_start: 0.9360 (mmmt) cc_final: 0.9102 (mmmm) REVERT: N 98 TYR cc_start: 0.7848 (m-10) cc_final: 0.7453 (m-80) REVERT: O 91 GLU cc_start: 0.8887 (pm20) cc_final: 0.8088 (pp20) REVERT: O 93 LEU cc_start: 0.9089 (tt) cc_final: 0.8842 (tt) REVERT: O 99 ARG cc_start: 0.7473 (mmm-85) cc_final: 0.7115 (tmm-80) REVERT: O 102 ILE cc_start: 0.7951 (mp) cc_final: 0.7704 (mm) REVERT: P 42 TYR cc_start: 0.8035 (t80) cc_final: 0.7834 (t80) REVERT: P 54 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7496 (pt) REVERT: P 62 MET cc_start: 0.9418 (mmm) cc_final: 0.9080 (tpp) REVERT: Q 90 MET cc_start: 0.7919 (mmp) cc_final: 0.7434 (mtt) REVERT: Q 94 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7688 (mt-10) REVERT: Q 97 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7945 (pp20) REVERT: Q 134 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7244 (ptm160) REVERT: R 44 LYS cc_start: 0.8058 (pptt) cc_final: 0.7807 (pptt) REVERT: R 50 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7638 (mm) REVERT: R 72 TYR cc_start: 0.9115 (m-80) cc_final: 0.8798 (m-80) REVERT: T 59 MET cc_start: 0.8562 (tpp) cc_final: 0.8230 (tpp) REVERT: T 70 PHE cc_start: 0.9160 (t80) cc_final: 0.8709 (t80) REVERT: T 71 GLU cc_start: 0.9424 (mm-30) cc_final: 0.8950 (mm-30) REVERT: T 79 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.7925 (ptm-80) REVERT: T 95 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8406 (tp40) REVERT: T 113 GLU cc_start: 0.8524 (tt0) cc_final: 0.7659 (pp20) outliers start: 123 outliers final: 75 residues processed: 634 average time/residue: 0.2579 time to fit residues: 269.8982 Evaluate side-chains 563 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 478 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 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 19 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 260 MET 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 343 ASP Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 199 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 426 ILE Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 149 ARG 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 113 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 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 650 VAL Chi-restraints excluded: chain G residue 668 LEU Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain G residue 1235 LEU Chi-restraints excluded: chain H residue 234 HIS Chi-restraints excluded: chain I residue 124 PHE Chi-restraints excluded: chain I residue 148 LEU 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 97 GLU Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain N residue 49 LEU 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 P residue 102 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 124 ILE Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 68 ASP 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 38 ASN Chi-restraints excluded: chain T residue 73 ILE Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 95 GLN 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: 6.9990 chunk 142 optimal weight: 0.9980 chunk 379 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 486 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 398 optimal weight: 10.0000 chunk 454 optimal weight: 40.0000 chunk 229 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 HIS D 313 ASN ** 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 ** O 31 HIS ** 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 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 HIS ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.112833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.073560 restraints weight = 106280.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075917 restraints weight = 47972.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.076551 restraints weight = 25956.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.077277 restraints weight = 18096.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.077277 restraints weight = 15809.724| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 44424 Z= 0.152 Angle : 0.624 9.727 61158 Z= 0.331 Chirality : 0.042 0.230 6942 Planarity : 0.004 0.059 6851 Dihedral : 21.486 162.584 8319 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.18 % Rotamer: Outliers : 3.00 % Allowed : 16.03 % Favored : 80.97 % 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: -0.16 (0.12), residues: 4675 helix: 0.52 (0.11), residues: 2222 sheet: -0.71 (0.20), residues: 565 loop : -0.52 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG O 35 TYR 0.020 0.001 TYR O 57 PHE 0.027 0.001 PHE M 67 TRP 0.020 0.001 TRP G1061 HIS 0.007 0.001 HIS T 49 Details of bonding type rmsd covalent geometry : bond 0.00346 (44424) covalent geometry : angle 0.62405 (61158) hydrogen bonds : bond 0.03830 ( 1957) hydrogen bonds : angle 4.21466 ( 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 640 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 519 time to evaluate : 1.532 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: 0.8833 (mmm) cc_final: 0.7803 (mmm) REVERT: A 99 SER cc_start: 0.8595 (t) cc_final: 0.8358 (t) REVERT: A 211 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8747 (p) REVERT: A 320 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: A 346 SER cc_start: 0.9279 (t) cc_final: 0.8948 (p) REVERT: B 114 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8199 (mt-10) REVERT: B 161 LEU cc_start: 0.8476 (mt) cc_final: 0.8247 (mt) REVERT: B 278 GLU cc_start: 0.7854 (tp30) cc_final: 0.7133 (tp30) REVERT: C 102 TYR cc_start: 0.8576 (m-10) cc_final: 0.7996 (m-80) REVERT: C 113 MET cc_start: 0.8217 (tpt) cc_final: 0.7952 (tpt) REVERT: C 371 MET cc_start: 0.8817 (tpp) cc_final: 0.8266 (mmt) REVERT: D 35 ASP cc_start: 0.8310 (m-30) cc_final: 0.8066 (t0) REVERT: D 147 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7979 (mm) REVERT: E 149 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6208 (tmm-80) REVERT: E 178 MET cc_start: 0.8655 (ttm) cc_final: 0.8345 (ttm) REVERT: E 201 LYS cc_start: 0.9181 (mttp) cc_final: 0.8932 (mtmm) REVERT: F 46 MET cc_start: 0.8244 (mtp) cc_final: 0.7958 (mtp) REVERT: F 162 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8263 (p) REVERT: F 174 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9123 (pp) REVERT: F 291 ILE cc_start: 0.9251 (mt) cc_final: 0.9043 (tt) REVERT: G 649 MET cc_start: 0.7826 (ptm) cc_final: 0.7332 (ppp) REVERT: G 688 MET cc_start: 0.8664 (mmp) cc_final: 0.8443 (mtt) REVERT: G 929 LEU cc_start: 0.9119 (tt) cc_final: 0.8818 (mt) REVERT: G 1148 ASP cc_start: 0.8305 (t0) cc_final: 0.7650 (p0) REVERT: H 215 LYS cc_start: 0.6409 (tttp) cc_final: 0.5954 (mmtt) REVERT: H 224 ARG cc_start: 0.7883 (tpp-160) cc_final: 0.7554 (tpp-160) REVERT: H 272 MET cc_start: 0.8604 (mmm) cc_final: 0.8107 (mmp) REVERT: H 327 GLN cc_start: 0.8028 (mp10) cc_final: 0.7777 (mp10) REVERT: I 145 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8567 (pttm) REVERT: I 187 ASN cc_start: 0.8747 (m-40) cc_final: 0.8511 (m-40) REVERT: I 194 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8801 (mmtm) REVERT: I 208 ARG cc_start: 0.8984 (ptp-110) cc_final: 0.8653 (ptp-110) REVERT: J 48 CYS cc_start: 0.8568 (t) cc_final: 0.8212 (p) REVERT: J 107 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6625 (pt0) REVERT: J 148 MET cc_start: 0.8965 (tpp) cc_final: 0.8751 (tpp) REVERT: J 481 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8486 (tptt) REVERT: J 486 MET cc_start: 0.8547 (tmm) cc_final: 0.8281 (tmm) REVERT: M 94 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8252 (tp30) REVERT: N 84 MET cc_start: 0.8504 (mmp) cc_final: 0.8254 (tmm) REVERT: N 88 TYR cc_start: 0.8291 (m-10) cc_final: 0.7875 (m-10) REVERT: N 91 LYS cc_start: 0.9355 (mmmt) cc_final: 0.9152 (mmmm) REVERT: N 98 TYR cc_start: 0.7850 (m-10) cc_final: 0.7480 (m-80) REVERT: O 90 ASP cc_start: 0.8190 (p0) cc_final: 0.7734 (t70) REVERT: O 91 GLU cc_start: 0.8888 (pm20) cc_final: 0.8151 (pp20) REVERT: P 54 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.6291 (pt) REVERT: P 62 MET cc_start: 0.9371 (mmm) cc_final: 0.8891 (tpp) REVERT: P 90 THR cc_start: 0.8881 (m) cc_final: 0.8608 (p) REVERT: P 102 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7329 (tt) REVERT: Q 90 MET cc_start: 0.7906 (mmp) cc_final: 0.7420 (mtt) REVERT: Q 94 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7812 (mt-10) REVERT: Q 122 LYS cc_start: 0.8645 (pttm) cc_final: 0.7812 (tppt) REVERT: Q 134 ARG cc_start: 0.7502 (mtt180) cc_final: 0.7248 (ptm160) REVERT: R 35 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.7975 (ttm-80) REVERT: R 63 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7564 (tm-30) REVERT: R 72 TYR cc_start: 0.9102 (m-80) cc_final: 0.8796 (m-80) REVERT: S 35 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7831 (mmm160) REVERT: T 46 LYS cc_start: 0.9172 (mmmt) cc_final: 0.8601 (mmmt) REVERT: T 70 PHE cc_start: 0.9130 (t80) cc_final: 0.8684 (t80) REVERT: T 71 GLU cc_start: 0.9454 (mm-30) cc_final: 0.8946 (mm-30) REVERT: T 79 ARG cc_start: 0.8428 (ttp-110) cc_final: 0.7955 (ptm-80) REVERT: T 95 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8381 (tp40) REVERT: T 113 GLU cc_start: 0.8484 (tt0) cc_final: 0.7623 (pp20) outliers start: 121 outliers final: 79 residues processed: 603 average time/residue: 0.2705 time to fit residues: 268.5347 Evaluate side-chains 563 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 473 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 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 19 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 308 ASP 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 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 147 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 199 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 426 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 149 ARG 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 174 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 209 PHE 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 668 LEU Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain G residue 1235 LEU 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 218 LEU Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 199 LEU 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 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 N residue 43 VAL Chi-restraints excluded: chain N residue 49 LEU 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 P residue 102 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 73 GLU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 68 ASP 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 94 ILE Chi-restraints excluded: chain T residue 95 GLN 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: 7.9990 chunk 113 optimal weight: 1.9990 chunk 448 optimal weight: 30.0000 chunk 360 optimal weight: 2.9990 chunk 339 optimal weight: 2.9990 chunk 344 optimal weight: 0.9990 chunk 416 optimal weight: 10.0000 chunk 356 optimal weight: 0.0370 chunk 395 optimal weight: 10.0000 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 675 ASN ** G1083 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 J 544 HIS M 108 ASN ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 GLN S 31 HIS ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN 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 = 0.113565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.075269 restraints weight = 104278.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.077030 restraints weight = 51738.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.077282 restraints weight = 31611.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.078038 restraints weight = 23538.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.078048 restraints weight = 19534.117| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 44424 Z= 0.189 Angle : 0.648 13.229 61158 Z= 0.341 Chirality : 0.043 0.203 6942 Planarity : 0.004 0.057 6851 Dihedral : 21.497 161.731 8319 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.08 % Favored : 96.83 % Rotamer: Outliers : 3.13 % Allowed : 16.45 % Favored : 80.42 % 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: -0.15 (0.12), residues: 4675 helix: 0.58 (0.11), residues: 2226 sheet: -0.76 (0.20), residues: 583 loop : -0.56 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 213 TYR 0.030 0.001 TYR N 72 PHE 0.024 0.001 PHE M 67 TRP 0.019 0.001 TRP G1061 HIS 0.021 0.001 HIS H 234 Details of bonding type rmsd covalent geometry : bond 0.00437 (44424) covalent geometry : angle 0.64802 (61158) hydrogen bonds : bond 0.03949 ( 1957) hydrogen bonds : angle 4.25462 ( 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 639 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 513 time to evaluate : 1.501 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: A 61 MET cc_start: 0.8608 (mmm) cc_final: 0.7764 (mmm) REVERT: A 99 SER cc_start: 0.8516 (t) cc_final: 0.8288 (t) REVERT: A 211 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8764 (p) REVERT: A 320 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7251 (mm-30) REVERT: A 346 SER cc_start: 0.9246 (t) cc_final: 0.9045 (p) REVERT: B 278 GLU cc_start: 0.7714 (tp30) cc_final: 0.7159 (tp30) REVERT: C 273 ASP cc_start: 0.8129 (t0) cc_final: 0.7865 (t0) REVERT: D 147 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8074 (mm) REVERT: E 149 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6687 (tmm-80) REVERT: F 174 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9230 (pp) REVERT: F 291 ILE cc_start: 0.9237 (mt) cc_final: 0.9035 (tt) REVERT: G 668 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8512 (mp) REVERT: G 1126 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.7950 (mtm) REVERT: G 1148 ASP cc_start: 0.8180 (t0) cc_final: 0.7816 (p0) REVERT: H 215 LYS cc_start: 0.6233 (tttp) cc_final: 0.5809 (mmtt) REVERT: H 224 ARG cc_start: 0.7827 (tpp-160) cc_final: 0.7469 (tpp-160) REVERT: H 272 MET cc_start: 0.8501 (mmm) cc_final: 0.7924 (mmp) REVERT: I 145 LYS cc_start: 0.8726 (ttmm) cc_final: 0.8473 (pttm) REVERT: I 194 LYS cc_start: 0.9122 (mmmt) cc_final: 0.8907 (mmtp) REVERT: J 107 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6479 (pt0) REVERT: M 94 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8219 (tp30) REVERT: N 62 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8817 (tp) REVERT: N 68 ASP cc_start: 0.8461 (m-30) cc_final: 0.8039 (t0) REVERT: N 72 TYR cc_start: 0.7125 (m-80) cc_final: 0.6304 (m-80) REVERT: N 98 TYR cc_start: 0.7754 (m-10) cc_final: 0.7553 (m-80) REVERT: O 91 GLU cc_start: 0.8876 (pm20) cc_final: 0.8130 (pp20) REVERT: O 92 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7432 (mt-10) REVERT: O 102 ILE cc_start: 0.8108 (mm) cc_final: 0.7731 (mp) REVERT: P 54 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7199 (pt) REVERT: P 62 MET cc_start: 0.9318 (mmm) cc_final: 0.8881 (tpp) REVERT: P 90 THR cc_start: 0.8935 (m) cc_final: 0.8533 (p) REVERT: P 102 LEU cc_start: 0.8294 (mt) cc_final: 0.7342 (tt) REVERT: Q 90 MET cc_start: 0.7898 (mmp) cc_final: 0.7389 (mtt) REVERT: Q 94 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7774 (mt-10) REVERT: Q 115 LYS cc_start: 0.8721 (mmtm) cc_final: 0.8475 (mppt) REVERT: Q 122 LYS cc_start: 0.8701 (pttm) cc_final: 0.7578 (tppt) REVERT: R 72 TYR cc_start: 0.9054 (m-80) cc_final: 0.8734 (m-80) REVERT: S 35 ARG cc_start: 0.8175 (mtm110) cc_final: 0.7800 (mmm160) REVERT: T 46 LYS cc_start: 0.9162 (mmmt) cc_final: 0.8569 (mmmt) REVERT: T 70 PHE cc_start: 0.8995 (t80) cc_final: 0.8595 (t80) REVERT: T 71 GLU cc_start: 0.9425 (mm-30) cc_final: 0.8900 (mm-30) REVERT: T 79 ARG cc_start: 0.8418 (ttp-110) cc_final: 0.7941 (ptm-80) REVERT: T 95 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8372 (tp40) REVERT: T 113 GLU cc_start: 0.8400 (tt0) cc_final: 0.7593 (pp20) outliers start: 126 outliers final: 87 residues processed: 599 average time/residue: 0.2825 time to fit residues: 277.3983 Evaluate side-chains 561 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 463 time to evaluate : 1.703 ------------------------------------------------------------------------------- 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 317 ARG Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 260 MET 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 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 147 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 199 THR 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 90 MET Chi-restraints excluded: chain E residue 149 ARG 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 405 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 209 PHE 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 668 LEU Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain G residue 1126 MET Chi-restraints excluded: chain G residue 1235 LEU 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 110 GLU Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 199 LEU 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 575 VAL Chi-restraints excluded: chain J residue 577 ILE Chi-restraints excluded: chain M residue 56 LYS Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain M residue 119 ILE Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 62 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 124 ILE Chi-restraints excluded: chain R residue 68 ASP 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 T residue 45 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 95 GLN 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: 0.3980 chunk 310 optimal weight: 0.9990 chunk 339 optimal weight: 7.9990 chunk 221 optimal weight: 0.0570 chunk 142 optimal weight: 0.7980 chunk 255 optimal weight: 3.9990 chunk 420 optimal weight: 0.2980 chunk 182 optimal weight: 5.9990 chunk 353 optimal weight: 9.9990 chunk 314 optimal weight: 0.8980 chunk 347 optimal weight: 20.0000 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 HIS ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1027 ASN ** G1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN O 31 HIS ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 ASN Q 108 ASN ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 HIS ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.113751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.074336 restraints weight = 108165.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.077071 restraints weight = 48547.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.077460 restraints weight = 26622.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.078074 restraints weight = 18213.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.078222 restraints weight = 15996.001| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 44424 Z= 0.134 Angle : 0.637 12.654 61158 Z= 0.335 Chirality : 0.042 0.243 6942 Planarity : 0.004 0.057 6851 Dihedral : 21.426 161.283 8319 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.28 % Rotamer: Outliers : 2.68 % Allowed : 17.59 % 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: -0.06 (0.12), residues: 4675 helix: 0.64 (0.11), residues: 2215 sheet: -0.72 (0.20), residues: 573 loop : -0.49 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG O 35 TYR 0.043 0.001 TYR N 88 PHE 0.026 0.001 PHE N 100 TRP 0.022 0.001 TRP G1061 HIS 0.004 0.001 HIS G 736 Details of bonding type rmsd covalent geometry : bond 0.00297 (44424) covalent geometry : angle 0.63651 (61158) hydrogen bonds : bond 0.03649 ( 1957) hydrogen bonds : angle 4.19359 ( 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 631 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 523 time to evaluate : 1.645 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: A 61 MET cc_start: 0.8785 (mmm) cc_final: 0.7999 (mmm) REVERT: A 99 SER cc_start: 0.8439 (t) cc_final: 0.8233 (t) REVERT: A 211 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8709 (p) REVERT: A 260 MET cc_start: 0.8538 (tpp) cc_final: 0.8336 (mmm) REVERT: A 346 SER cc_start: 0.9271 (t) cc_final: 0.8918 (p) REVERT: B 186 GLU cc_start: 0.7220 (pp20) cc_final: 0.6825 (pp20) REVERT: B 278 GLU cc_start: 0.7861 (tp30) cc_final: 0.7164 (tp30) REVERT: B 306 MET cc_start: 0.8237 (ptp) cc_final: 0.8001 (ptp) REVERT: C 278 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8014 (mm-30) REVERT: D 147 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7924 (mm) REVERT: D 430 TYR cc_start: 0.8519 (t80) cc_final: 0.8266 (t80) REVERT: E 149 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6163 (tmm-80) REVERT: F 162 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8204 (p) REVERT: F 174 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9162 (pp) REVERT: G 649 MET cc_start: 0.7862 (ptm) cc_final: 0.7293 (ppp) REVERT: G 668 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8627 (mp) REVERT: G 688 MET cc_start: 0.8246 (mtt) cc_final: 0.7948 (mtm) REVERT: G 1126 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8021 (mtm) REVERT: G 1148 ASP cc_start: 0.8281 (t0) cc_final: 0.7537 (p0) REVERT: H 215 LYS cc_start: 0.6491 (tttp) cc_final: 0.6001 (mmtt) REVERT: H 224 ARG cc_start: 0.8043 (tpp-160) cc_final: 0.7681 (tpp-160) REVERT: H 272 MET cc_start: 0.8643 (mmm) cc_final: 0.8045 (mmp) REVERT: H 298 GLN cc_start: 0.8026 (tp-100) cc_final: 0.7696 (tp-100) REVERT: H 327 GLN cc_start: 0.8061 (mp10) cc_final: 0.7848 (mp10) REVERT: I 145 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8403 (pttm) REVERT: I 152 ARG cc_start: 0.7898 (tpp80) cc_final: 0.7346 (mpt-90) REVERT: J 48 CYS cc_start: 0.8693 (t) cc_final: 0.8139 (p) REVERT: J 107 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: J 486 MET cc_start: 0.8569 (tmm) cc_final: 0.8348 (tmm) REVERT: M 94 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8321 (tp30) REVERT: N 58 LEU cc_start: 0.9193 (tp) cc_final: 0.8801 (pp) REVERT: N 62 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8685 (tp) REVERT: N 68 ASP cc_start: 0.8462 (m-30) cc_final: 0.7930 (t0) REVERT: N 91 LYS cc_start: 0.9329 (mmmt) cc_final: 0.9032 (mmmm) REVERT: O 63 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8493 (pp) REVERT: O 91 GLU cc_start: 0.9025 (pm20) cc_final: 0.8170 (pp20) REVERT: O 92 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7447 (mt-10) REVERT: O 102 ILE cc_start: 0.8088 (mm) cc_final: 0.7707 (mp) REVERT: P 54 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7216 (pt) REVERT: P 62 MET cc_start: 0.9420 (mmm) cc_final: 0.9000 (tpp) REVERT: P 90 THR cc_start: 0.8746 (m) cc_final: 0.8299 (p) REVERT: P 102 LEU cc_start: 0.8340 (mt) cc_final: 0.7423 (tt) REVERT: Q 90 MET cc_start: 0.7878 (mmp) cc_final: 0.6953 (mtt) REVERT: Q 94 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7665 (mp0) REVERT: Q 115 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8521 (mppt) REVERT: Q 122 LYS cc_start: 0.8582 (pttm) cc_final: 0.7871 (tppt) REVERT: R 63 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7720 (tm-30) REVERT: R 72 TYR cc_start: 0.9070 (m-80) cc_final: 0.8730 (m-80) REVERT: R 91 LYS cc_start: 0.9111 (tptt) cc_final: 0.8367 (mtpt) REVERT: S 73 ASN cc_start: 0.8739 (t0) cc_final: 0.8382 (m-40) REVERT: T 46 LYS cc_start: 0.9213 (mmmt) cc_final: 0.8644 (mmmt) REVERT: T 70 PHE cc_start: 0.9098 (t80) cc_final: 0.8771 (t80) REVERT: T 71 GLU cc_start: 0.9499 (mm-30) cc_final: 0.9211 (mm-30) REVERT: T 79 ARG cc_start: 0.8362 (ttp-110) cc_final: 0.7854 (ptm-80) REVERT: T 95 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8390 (tp40) REVERT: T 113 GLU cc_start: 0.8370 (tt0) cc_final: 0.7557 (pp20) outliers start: 108 outliers final: 75 residues processed: 591 average time/residue: 0.2515 time to fit residues: 246.0146 Evaluate side-chains 561 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 474 time to evaluate : 1.542 ------------------------------------------------------------------------------- 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 211 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 137 GLU 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 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 147 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 398 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 182 LEU 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 603 HIS Chi-restraints excluded: chain G residue 650 VAL Chi-restraints excluded: chain G residue 668 LEU Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1126 MET Chi-restraints excluded: chain G residue 1235 LEU Chi-restraints excluded: chain I residue 124 PHE Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 233 HIS Chi-restraints excluded: chain J residue 444 VAL 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 97 GLU Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 119 ILE Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 25 PHE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 63 LEU 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 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 47 SER Chi-restraints excluded: chain R residue 68 ASP 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 45 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 95 GLN Chi-restraints excluded: chain T residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 4 optimal weight: 0.0020 chunk 418 optimal weight: 20.0000 chunk 366 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 302 optimal weight: 5.9990 chunk 325 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 396 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 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** M 108 ASN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.114716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.077082 restraints weight = 104462.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.078173 restraints weight = 49549.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.078930 restraints weight = 28946.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.078895 restraints weight = 27053.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.079043 restraints weight = 24321.902| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 44424 Z= 0.154 Angle : 0.635 13.225 61158 Z= 0.334 Chirality : 0.042 0.262 6942 Planarity : 0.004 0.058 6851 Dihedral : 21.387 160.490 8319 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.91 % Favored : 96.98 % Rotamer: Outliers : 2.48 % Allowed : 17.97 % Favored : 79.55 % 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: -0.06 (0.12), residues: 4675 helix: 0.64 (0.11), residues: 2239 sheet: -0.70 (0.20), residues: 577 loop : -0.50 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 35 TYR 0.053 0.001 TYR N 98 PHE 0.026 0.001 PHE N 100 TRP 0.019 0.001 TRP G1061 HIS 0.008 0.001 HIS H 234 Details of bonding type rmsd covalent geometry : bond 0.00352 (44424) covalent geometry : angle 0.63543 (61158) hydrogen bonds : bond 0.03711 ( 1957) hydrogen bonds : angle 4.21670 ( 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 581 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 481 time to evaluate : 1.522 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 61 MET cc_start: 0.8583 (mmm) cc_final: 0.7815 (mmm) REVERT: A 211 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8699 (p) REVERT: A 320 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7182 (mm-30) REVERT: A 346 SER cc_start: 0.9205 (t) cc_final: 0.9003 (p) REVERT: B 186 GLU cc_start: 0.7242 (pp20) cc_final: 0.6885 (pp20) REVERT: B 278 GLU cc_start: 0.7702 (tp30) cc_final: 0.7132 (tp30) REVERT: D 147 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8003 (mm) REVERT: D 430 TYR cc_start: 0.8570 (t80) cc_final: 0.8308 (t80) REVERT: E 149 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6419 (tmm-80) REVERT: F 174 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9280 (pp) REVERT: G 688 MET cc_start: 0.7841 (mtt) cc_final: 0.7522 (mtm) REVERT: G 1126 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8058 (mtm) REVERT: G 1148 ASP cc_start: 0.8027 (t0) cc_final: 0.7699 (p0) REVERT: H 215 LYS cc_start: 0.6263 (tttp) cc_final: 0.5812 (mmtt) REVERT: H 272 MET cc_start: 0.8530 (mmm) cc_final: 0.8155 (mmp) REVERT: H 298 GLN cc_start: 0.7771 (tp-100) cc_final: 0.7520 (tp-100) REVERT: I 145 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8324 (pttm) REVERT: J 48 CYS cc_start: 0.8507 (t) cc_final: 0.8136 (p) REVERT: J 107 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: M 94 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8076 (tp30) REVERT: N 58 LEU cc_start: 0.9151 (tp) cc_final: 0.8736 (pp) REVERT: N 62 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8564 (tp) REVERT: N 68 ASP cc_start: 0.8321 (m-30) cc_final: 0.7955 (t0) REVERT: N 91 LYS cc_start: 0.9307 (mmmt) cc_final: 0.9022 (mmmm) REVERT: N 98 TYR cc_start: 0.7335 (m-10) cc_final: 0.7091 (m-80) REVERT: O 91 GLU cc_start: 0.8763 (pm20) cc_final: 0.8004 (pp20) REVERT: O 92 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7076 (mt-10) REVERT: O 102 ILE cc_start: 0.7970 (mm) cc_final: 0.7590 (mp) REVERT: P 54 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7271 (pt) REVERT: P 59 MET cc_start: 0.8406 (mmm) cc_final: 0.8116 (mmm) REVERT: P 90 THR cc_start: 0.8860 (m) cc_final: 0.8414 (p) REVERT: P 102 LEU cc_start: 0.8143 (mt) cc_final: 0.7230 (tt) REVERT: Q 90 MET cc_start: 0.7835 (mmp) cc_final: 0.6737 (mtt) REVERT: Q 94 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7560 (mp0) REVERT: Q 122 LYS cc_start: 0.8532 (pttm) cc_final: 0.7844 (tppt) REVERT: R 72 TYR cc_start: 0.8952 (m-80) cc_final: 0.8628 (m-80) REVERT: S 75 LYS cc_start: 0.7815 (mmmm) cc_final: 0.7484 (mmmt) REVERT: T 46 LYS cc_start: 0.9175 (mmmt) cc_final: 0.8637 (mmmt) REVERT: T 70 PHE cc_start: 0.8767 (t80) cc_final: 0.8530 (t80) REVERT: T 79 ARG cc_start: 0.8423 (ttp-110) cc_final: 0.7963 (ptm-80) REVERT: T 95 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8473 (tp40) REVERT: T 113 GLU cc_start: 0.8218 (tt0) cc_final: 0.7567 (pp20) outliers start: 100 outliers final: 82 residues processed: 547 average time/residue: 0.2513 time to fit residues: 228.7273 Evaluate side-chains 552 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 460 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 211 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain C residue 66 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 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 147 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 398 SER Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 326 MET 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 648 TYR Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain G residue 1126 MET Chi-restraints excluded: chain G residue 1235 LEU Chi-restraints excluded: chain I residue 124 PHE Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 166 ILE 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 110 GLU Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 233 HIS Chi-restraints excluded: chain J residue 444 VAL 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 97 GLU Chi-restraints excluded: chain M residue 119 ILE Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 25 PHE 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 68 GLN Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 68 ASP 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 83 LEU Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 95 GLN Chi-restraints excluded: chain T residue 96 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 93 optimal weight: 0.0470 chunk 245 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 249 optimal weight: 0.4980 chunk 294 optimal weight: 0.8980 chunk 327 optimal weight: 30.0000 chunk 68 optimal weight: 0.0060 chunk 261 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 264 optimal weight: 0.5980 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 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** ** G1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN O 73 ASN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.116405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.079517 restraints weight = 104395.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.080680 restraints weight = 49281.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.080902 restraints weight = 29972.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.081226 restraints weight = 27472.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.081492 restraints weight = 25562.358| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 44424 Z= 0.132 Angle : 0.657 14.957 61158 Z= 0.342 Chirality : 0.042 0.282 6942 Planarity : 0.004 0.058 6851 Dihedral : 21.327 159.980 8319 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 2.31 % Allowed : 18.49 % Favored : 79.21 % 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: -0.04 (0.12), residues: 4675 helix: 0.67 (0.11), residues: 2233 sheet: -0.69 (0.21), residues: 572 loop : -0.52 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 229 TYR 0.036 0.001 TYR N 98 PHE 0.028 0.001 PHE N 100 TRP 0.021 0.001 TRP G1061 HIS 0.007 0.001 HIS H 234 Details of bonding type rmsd covalent geometry : bond 0.00286 (44424) covalent geometry : angle 0.65667 (61158) hydrogen bonds : bond 0.03605 ( 1957) hydrogen bonds : angle 4.20681 ( 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: 93 poor density : 511 time to evaluate : 1.723 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: A 61 MET cc_start: 0.8604 (mmm) cc_final: 0.7852 (mmm) REVERT: A 211 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8630 (p) REVERT: A 287 ILE cc_start: 0.9314 (pt) cc_final: 0.9021 (mt) REVERT: A 320 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7004 (mm-30) REVERT: B 186 GLU cc_start: 0.7342 (pp20) cc_final: 0.7065 (pp20) REVERT: B 278 GLU cc_start: 0.7695 (tp30) cc_final: 0.7136 (tp30) REVERT: C 273 ASP cc_start: 0.7976 (t0) cc_final: 0.7769 (t0) REVERT: D 160 LYS cc_start: 0.8977 (mmtm) cc_final: 0.8410 (mtpp) REVERT: D 430 TYR cc_start: 0.8490 (t80) cc_final: 0.8231 (t80) REVERT: E 149 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6359 (tmm-80) REVERT: F 162 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8394 (p) REVERT: F 174 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9274 (pp) REVERT: G 688 MET cc_start: 0.7793 (mtt) cc_final: 0.7459 (mtm) REVERT: G 699 MET cc_start: 0.6138 (mmm) cc_final: 0.5873 (mmp) REVERT: G 822 PHE cc_start: 0.8399 (t80) cc_final: 0.8044 (m-80) REVERT: G 1048 GLN cc_start: 0.8210 (mt0) cc_final: 0.7681 (mp10) REVERT: G 1126 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8093 (mtm) REVERT: G 1148 ASP cc_start: 0.7982 (t0) cc_final: 0.7614 (p0) REVERT: H 215 LYS cc_start: 0.6247 (tttp) cc_final: 0.5862 (mmtt) REVERT: H 272 MET cc_start: 0.8568 (mmm) cc_final: 0.8174 (mmp) REVERT: H 298 GLN cc_start: 0.7660 (tp-100) cc_final: 0.7423 (tp-100) REVERT: I 152 ARG cc_start: 0.7638 (tpp80) cc_final: 0.7092 (mpt-90) REVERT: J 48 CYS cc_start: 0.8444 (t) cc_final: 0.8130 (p) REVERT: J 107 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: M 94 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8098 (tp30) REVERT: N 30 THR cc_start: 0.8573 (p) cc_final: 0.8253 (t) REVERT: N 58 LEU cc_start: 0.9140 (tp) cc_final: 0.8741 (pp) REVERT: N 62 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8605 (tt) REVERT: N 68 ASP cc_start: 0.8220 (m-30) cc_final: 0.7888 (t0) REVERT: N 77 LYS cc_start: 0.7434 (mmtt) cc_final: 0.6694 (mttm) REVERT: N 91 LYS cc_start: 0.9286 (mmmt) cc_final: 0.8997 (mmmm) REVERT: O 91 GLU cc_start: 0.8730 (pm20) cc_final: 0.7932 (pp20) REVERT: O 92 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6900 (mt-10) REVERT: P 54 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7095 (pt) REVERT: P 59 MET cc_start: 0.8439 (mmm) cc_final: 0.8180 (mmm) REVERT: P 90 THR cc_start: 0.8793 (m) cc_final: 0.8344 (p) REVERT: P 100 LEU cc_start: 0.9246 (mt) cc_final: 0.8979 (tp) REVERT: P 102 LEU cc_start: 0.8266 (mt) cc_final: 0.7386 (tt) REVERT: Q 90 MET cc_start: 0.7864 (mmp) cc_final: 0.6808 (mtt) REVERT: Q 94 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7642 (mp0) REVERT: Q 122 LYS cc_start: 0.8529 (pttm) cc_final: 0.7847 (tppt) REVERT: R 91 LYS cc_start: 0.9224 (mmtt) cc_final: 0.8420 (mtpt) REVERT: T 46 LYS cc_start: 0.9185 (mmmt) cc_final: 0.8684 (mmmt) REVERT: T 70 PHE cc_start: 0.8767 (t80) cc_final: 0.8435 (t80) REVERT: T 113 GLU cc_start: 0.8218 (tt0) cc_final: 0.7649 (pp20) outliers start: 93 outliers final: 70 residues processed: 568 average time/residue: 0.2612 time to fit residues: 246.6803 Evaluate side-chains 553 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 474 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 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 19 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain C residue 66 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 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 161 LEU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 199 THR 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 174 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 326 MET 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 G residue 593 PHE Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain G residue 1126 MET Chi-restraints excluded: chain G residue 1235 LEU 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 444 VAL Chi-restraints excluded: chain J residue 468 ILE Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 25 PHE 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 68 GLN Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 47 SER 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 83 LEU Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 95 GLN 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: 0.3980 chunk 61 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 233 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 chunk 283 optimal weight: 10.0000 chunk 204 optimal weight: 0.8980 chunk 296 optimal weight: 0.8980 chunk 452 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN ** B 156 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** ** G1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN O 73 ASN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN T 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.114061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.074924 restraints weight = 108608.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.077593 restraints weight = 49952.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.077986 restraints weight = 24177.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.078335 restraints weight = 20489.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.078484 restraints weight = 18417.228| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 44424 Z= 0.142 Angle : 0.647 13.215 61158 Z= 0.338 Chirality : 0.042 0.296 6942 Planarity : 0.004 0.060 6851 Dihedral : 21.295 159.347 8318 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.92 % Rotamer: Outliers : 2.16 % Allowed : 18.76 % Favored : 79.08 % 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: 0.01 (0.12), residues: 4675 helix: 0.70 (0.11), residues: 2235 sheet: -0.67 (0.20), residues: 572 loop : -0.48 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG R 67 TYR 0.050 0.001 TYR N 98 PHE 0.025 0.001 PHE N 100 TRP 0.018 0.001 TRP G1061 HIS 0.006 0.001 HIS H 234 Details of bonding type rmsd covalent geometry : bond 0.00322 (44424) covalent geometry : angle 0.64717 (61158) hydrogen bonds : bond 0.03640 ( 1957) hydrogen bonds : angle 4.21106 ( 5316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9623.82 seconds wall clock time: 166 minutes 13.04 seconds (9973.04 seconds total)