Starting phenix.real_space_refine on Fri Jun 5 09:42:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5oaf_3773/06_2026/5oaf_3773_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5oaf_3773/06_2026/5oaf_3773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5oaf_3773/06_2026/5oaf_3773_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5oaf_3773/06_2026/5oaf_3773_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5oaf_3773/06_2026/5oaf_3773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5oaf_3773/06_2026/5oaf_3773.map" } resolution = 4.06 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 92 5.16 5 C 12342 2.51 5 N 3434 2.21 5 O 3868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19748 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3357 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 16, 'TRANS': 419} Chain breaks: 1 Chain: "B" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3232 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "C" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3253 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 16, 'TRANS': 407} Chain breaks: 1 Chain: "D" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3187 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 10, 'TRANS': 400} Chain breaks: 2 Chain: "E" Number of atoms: 3400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3400 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 17, 'TRANS': 424} Chain: "F" Number of atoms: 3157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3157 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 10, 'TRANS': 396} Chain breaks: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.56, per 1000 atoms: 0.23 Number of scatterers: 19748 At special positions: 0 Unit cell: (131.44, 127.2, 132.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 12 15.00 O 3868 8.00 N 3434 7.00 C 12342 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: 1.42 Conformation dependent library (CDL) restraints added in 903.0 milliseconds 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4668 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 32 sheets defined 45.9% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.746A pdb=" N ILE A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 53 " --> pdb=" O CYS A 49 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.529A pdb=" N GLY A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 removed outlier: 4.012A pdb=" N ILE A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 256 through 263 removed outlier: 3.827A pdb=" N MET A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 289 removed outlier: 3.586A pdb=" N GLY A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.809A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 383 Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 402 through 421 removed outlier: 3.777A pdb=" N SER A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.387A 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: 3.957A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 447 Processing helix chain 'B' and resid 49 through 66 removed outlier: 3.560A pdb=" N GLY B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.815A pdb=" N ILE B 86 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 removed outlier: 3.602A pdb=" N ILE B 127 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 185 Processing helix chain 'B' and resid 205 through 211 removed outlier: 4.375A pdb=" N PHE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 252 Processing helix chain 'B' and resid 254 through 261 removed outlier: 4.452A pdb=" N LEU B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 284 Processing helix chain 'B' and resid 305 through 318 removed outlier: 3.760A pdb=" N ASN B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 346 Processing helix chain 'B' and resid 347 through 354 removed outlier: 3.552A pdb=" N ARG B 353 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 378 removed outlier: 3.859A pdb=" N LYS B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 398 through 416 removed outlier: 3.608A pdb=" N ALA B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 433 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.069A pdb=" N LYS B 444 " --> pdb=" O GLN B 441 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU B 445 " --> pdb=" O TYR B 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 4.032A pdb=" N VAL C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 88 removed outlier: 3.502A pdb=" N GLY C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.759A pdb=" N VAL C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 183 removed outlier: 4.088A pdb=" N LYS C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 254 through 263 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 276 through 290 removed outlier: 3.939A pdb=" N GLN C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.590A pdb=" N PHE C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 358 removed outlier: 3.886A pdb=" N ARG C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 383 removed outlier: 3.559A pdb=" N LYS C 376 " --> pdb=" O LYS C 372 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 381 " --> pdb=" O ILE C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.857A pdb=" N SER C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 421 removed outlier: 3.663A pdb=" N ALA C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 437 Processing helix chain 'C' and resid 439 through 447 Processing helix chain 'D' and resid 24 through 28 removed outlier: 4.126A pdb=" N HIS D 27 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE D 28 " --> pdb=" O HIS D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 28' Processing helix chain 'D' and resid 42 through 46 removed outlier: 3.960A pdb=" N GLY D 45 " --> pdb=" O ALA D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.814A pdb=" N GLY D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 removed outlier: 3.824A pdb=" N ALA D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.506A pdb=" N PHE D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 105 through 109' Processing helix chain 'D' and resid 114 through 127 removed outlier: 3.630A pdb=" N ILE D 127 " --> pdb=" O PHE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 222 through 226 removed outlier: 4.089A pdb=" N VAL D 225 " --> pdb=" O THR D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 252 removed outlier: 3.552A pdb=" N ASN D 251 " --> pdb=" O ILE D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 removed outlier: 3.636A pdb=" N LEU D 258 " --> pdb=" O THR D 254 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 286 removed outlier: 3.713A pdb=" N ILE D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.577A pdb=" N PHE D 309 " --> pdb=" O ASP D 305 " (cutoff:3.500A) removed outlier: 3.675A 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 354 Processing helix chain 'D' and resid 363 through 378 removed outlier: 3.636A pdb=" N LYS D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG D 374 " --> pdb=" O ILE D 370 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N CYS D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 397 removed outlier: 4.120A pdb=" N VAL D 389 " --> pdb=" O ASP D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 416 removed outlier: 3.532A pdb=" N ALA D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 435 through 442 Processing helix chain 'D' and resid 443 through 446 Processing helix chain 'E' and resid 42 through 59 removed outlier: 3.917A pdb=" N ILE E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL E 53 " --> pdb=" O CYS E 49 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU E 55 " --> pdb=" O VAL E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 88 removed outlier: 4.545A pdb=" N ALA E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 102 Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.639A pdb=" N ILE E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 removed outlier: 4.078A pdb=" N GLU E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 249 Processing helix chain 'E' and resid 256 through 263 removed outlier: 4.044A pdb=" N MET E 260 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 290 removed outlier: 3.516A pdb=" N ARG E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 320 removed outlier: 3.542A pdb=" N PHE E 312 " --> pdb=" O ASP E 308 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 350 Processing helix chain 'E' and resid 351 through 358 removed outlier: 3.998A pdb=" N ARG E 357 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 383 removed outlier: 4.422A pdb=" N GLN E 373 " --> pdb=" O GLN E 369 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE E 377 " --> pdb=" O GLN E 373 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG E 378 " --> pdb=" O ILE E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 401 Processing helix chain 'E' and resid 402 through 409 removed outlier: 3.816A pdb=" N SER E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 421 removed outlier: 3.841A pdb=" N ALA E 413 " --> pdb=" O LEU E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 437 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 114 through 126 removed outlier: 3.622A pdb=" N ALA F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 185 removed outlier: 4.164A pdb=" N GLU F 180 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER F 181 " --> pdb=" O LYS F 177 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS F 184 " --> pdb=" O GLU F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 252 Processing helix chain 'F' and resid 254 through 261 removed outlier: 4.350A pdb=" N LEU F 258 " --> pdb=" O THR F 254 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE F 261 " --> pdb=" O PHE F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 287 removed outlier: 3.616A pdb=" N VAL F 272 " --> pdb=" O ILE F 268 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE F 276 " --> pdb=" O VAL F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 318 removed outlier: 3.729A pdb=" N ASN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 346 Processing helix chain 'F' and resid 347 through 352 removed outlier: 3.974A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 376 removed outlier: 3.818A pdb=" N LYS F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 397 removed outlier: 3.721A pdb=" N VAL F 389 " --> pdb=" O ASP F 385 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU F 396 " --> pdb=" O ARG F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.533A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU F 411 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 removed outlier: 3.507A pdb=" N SER F 431 " --> pdb=" O LYS F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 442 removed outlier: 3.984A pdb=" N GLN F 441 " --> pdb=" O SER F 437 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR F 442 " --> pdb=" O ARG F 438 " (cutoff:3.500A) 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: 3.548A pdb=" N CYS A 94 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 300 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU A 299 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ALA A 330 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL A 301 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 172 removed outlier: 3.602A pdb=" N GLU A 134 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.696A pdb=" N ASP A 189 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 337 removed outlier: 3.527A pdb=" N CYS A 336 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 104 removed outlier: 6.158A pdb=" N LEU B 296 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA B 327 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 298 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 77 " --> pdb=" O THR B 328 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 355 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 239 through 243 Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 164 Processing sheet with id=AB1, first strand: chain 'B' and resid 193 through 195 removed outlier: 4.044A pdb=" N ILE B 202 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 333 through 334 removed outlier: 3.558A pdb=" N THR B 333 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 342 " --> pdb=" O THR B 333 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB4, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.473A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL C 66 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N SER C 331 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU C 68 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 200 through 201 removed outlier: 3.882A pdb=" N VAL C 200 " --> pdb=" O TYR C 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 201 removed outlier: 3.882A pdb=" N VAL C 200 " --> pdb=" O TYR C 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 134 through 137 Processing sheet with id=AB8, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AB9, first strand: chain 'D' and resid 100 through 104 removed outlier: 3.806A pdb=" N ASP D 299 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU D 296 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA D 327 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE D 298 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY D 77 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU D 355 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 240 through 243 removed outlier: 3.562A pdb=" N ILE D 131 " --> pdb=" O HIS D 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 201 through 203 removed outlier: 3.895A pdb=" N ILE D 202 " --> pdb=" O THR D 194 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 138 " --> pdb=" O ILE D 195 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 141 through 145 removed outlier: 3.685A pdb=" N ILE D 145 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS D 160 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU D 161 " --> pdb=" O TYR D 172 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR D 172 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 333 through 334 removed outlier: 3.518A pdb=" N SER D 342 " --> pdb=" O THR D 333 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AC6, first strand: chain 'E' and resid 93 through 95 removed outlier: 3.528A pdb=" N CYS E 94 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE E 300 " --> pdb=" O CYS E 94 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU E 299 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ALA E 330 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL E 301 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL E 66 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER E 331 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU E 68 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET E 359 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 193 through 194 Processing sheet with id=AC8, first strand: chain 'E' and resid 193 through 194 Processing sheet with id=AC9, first strand: chain 'E' and resid 157 through 163 removed outlier: 3.688A pdb=" N VAL E 157 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AD2, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.615A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 200 through 203 removed outlier: 3.589A pdb=" N VAL F 238 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS F 236 " --> pdb=" O THR F 135 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 200 through 203 Processing sheet with id=AD5, first strand: chain 'F' and resid 143 through 145 removed outlier: 3.582A pdb=" N LYS F 160 " --> pdb=" O ILE F 145 " (cutoff:3.500A) 845 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6639 1.34 - 1.46: 3384 1.46 - 1.58: 9789 1.58 - 1.69: 18 1.69 - 1.81: 160 Bond restraints: 19990 Sorted by residual: bond pdb=" C CYS D 227 " pdb=" N PRO D 228 " ideal model delta sigma weight residual 1.334 1.371 -0.038 2.34e-02 1.83e+03 2.58e+00 bond pdb=" C ASP E 273 " pdb=" N LYS E 274 " ideal model delta sigma weight residual 1.335 1.319 0.016 1.38e-02 5.25e+03 1.31e+00 bond pdb=" N GLN E 251 " pdb=" CA GLN E 251 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.14e+00 bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" C GLY A 198 " pdb=" N ALA A 199 " ideal model delta sigma weight residual 1.331 1.319 0.013 1.29e-02 6.01e+03 1.01e+00 ... (remaining 19985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 26698 2.08 - 4.15: 196 4.15 - 6.23: 55 6.23 - 8.31: 0 8.31 - 10.39: 1 Bond angle restraints: 26950 Sorted by residual: angle pdb=" N LEU E 315 " pdb=" CA LEU E 315 " pdb=" C LEU E 315 " ideal model delta sigma weight residual 111.28 106.26 5.02 1.09e+00 8.42e-01 2.12e+01 angle pdb=" CA LEU B 232 " pdb=" CB LEU B 232 " pdb=" CG LEU B 232 " ideal model delta sigma weight residual 116.30 126.69 -10.39 3.50e+00 8.16e-02 8.81e+00 angle pdb=" C ASP A 356 " pdb=" N ARG A 357 " pdb=" CA ARG A 357 " ideal model delta sigma weight residual 121.54 126.97 -5.43 1.91e+00 2.74e-01 8.09e+00 angle pdb=" N ALA F 198 " pdb=" CA ALA F 198 " pdb=" C ALA F 198 " ideal model delta sigma weight residual 113.19 109.84 3.35 1.19e+00 7.06e-01 7.92e+00 angle pdb=" N GLY A 253 " pdb=" CA GLY A 253 " pdb=" C GLY A 253 " ideal model delta sigma weight residual 110.87 114.69 -3.82 1.54e+00 4.22e-01 6.15e+00 ... (remaining 26945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.58: 12275 30.58 - 61.16: 71 61.16 - 91.73: 0 91.73 - 122.31: 4 122.31 - 152.89: 10 Dihedral angle restraints: 12360 sinusoidal: 5113 harmonic: 7247 Sorted by residual: dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 92.89 -152.89 1 2.00e+01 2.50e-03 4.54e+01 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 -60.00 89.33 -149.32 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O2A ADP B 501 " pdb=" O3A ADP B 501 " pdb=" PA ADP B 501 " pdb=" PB ADP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 72.88 -132.88 1 2.00e+01 2.50e-03 4.03e+01 ... (remaining 12357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2172 0.031 - 0.061: 635 0.061 - 0.092: 136 0.092 - 0.123: 215 0.123 - 0.153: 12 Chirality restraints: 3170 Sorted by residual: chirality pdb=" CA TYR E 314 " pdb=" N TYR E 314 " pdb=" C TYR E 314 " pdb=" CB TYR E 314 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA ILE E 350 " pdb=" N ILE E 350 " pdb=" C ILE E 350 " pdb=" CB ILE E 350 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE A 256 " pdb=" N ILE A 256 " pdb=" C ILE A 256 " pdb=" CB ILE A 256 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 3167 not shown) Planarity restraints: 3434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 139 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO C 140 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 140 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 140 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 295 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 296 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 296 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 296 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 98 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO F 99 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO F 99 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 99 " -0.021 5.00e-02 4.00e+02 ... (remaining 3431 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 494 2.71 - 3.26: 20009 3.26 - 3.81: 28601 3.81 - 4.35: 37657 4.35 - 4.90: 61523 Nonbonded interactions: 148284 Sorted by model distance: nonbonded pdb=" OG1 THR A 367 " pdb=" OE1 GLU A 370 " model vdw 2.165 3.040 nonbonded pdb=" O TYR B 387 " pdb=" OG1 THR B 391 " model vdw 2.201 3.040 nonbonded pdb=" O TYR D 387 " pdb=" OG1 THR D 391 " model vdw 2.209 3.040 nonbonded pdb=" NH1 ARG F 400 " pdb=" O2A ADP F 501 " model vdw 2.212 3.120 nonbonded pdb=" OG SER E 99 " pdb=" OG SER F 310 " model vdw 2.235 3.040 ... (remaining 148279 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 11 through 205 or resid 224 through 501)) selection = (chain 'C' and (resid 11 through 144 or resid 151 through 501)) selection = (chain 'E' and (resid 11 through 144 or resid 151 through 205 or resid 224 throu \ gh 501)) } ncs_group { reference = (chain 'B' and (resid 16 through 146 or resid 159 through 210 or resid 228 throu \ gh 501)) selection = (chain 'D' and (resid 16 through 210 or resid 228 through 501)) selection = (chain 'F' and (resid 16 through 449 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.100 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 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 : 0.001 0.038 19990 Z= 0.085 Angle : 0.475 10.387 26950 Z= 0.255 Chirality : 0.040 0.153 3170 Planarity : 0.003 0.052 3434 Dihedral : 9.128 152.889 7692 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.28 % Allowed : 0.05 % Favored : 99.67 % 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: -2.75 (0.13), residues: 2512 helix: -2.78 (0.11), residues: 1006 sheet: -0.45 (0.20), residues: 428 loop : -1.20 (0.16), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 400 TYR 0.007 0.001 TYR E 314 PHE 0.007 0.001 PHE D 224 TRP 0.003 0.000 TRP B 283 HIS 0.002 0.000 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00148 / 0.08 (19990) covalent geometry : angle 0.47492 / 0.25 (26950) hydrogen bonds : bond 0.16247 / 10.42 ( 832) hydrogen bonds : angle 9.76381 / 6.73 ( 2382) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 759 time to evaluate : 0.858 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: A 184 ARG cc_start: 0.7324 (mpt180) cc_final: 0.6510 (mtp180) REVERT: A 215 LEU cc_start: 0.6942 (mt) cc_final: 0.6435 (tt) REVERT: A 260 MET cc_start: 0.6668 (ptm) cc_final: 0.6131 (ppp) REVERT: A 298 VAL cc_start: 0.6472 (t) cc_final: 0.6113 (t) REVERT: B 117 GLU cc_start: 0.8280 (tm-30) cc_final: 0.8013 (tm-30) REVERT: B 141 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6733 (pp20) REVERT: B 168 MET cc_start: 0.4892 (mmm) cc_final: 0.4651 (ttt) REVERT: B 174 LEU cc_start: 0.7024 (mt) cc_final: 0.6556 (mt) REVERT: B 199 THR cc_start: 0.7066 (p) cc_final: 0.6810 (m) REVERT: B 232 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6755 (pp) REVERT: C 271 ILE cc_start: 0.8452 (mm) cc_final: 0.8234 (mm) REVERT: C 332 ASN cc_start: 0.8119 (t0) cc_final: 0.7833 (t0) REVERT: C 359 MET cc_start: 0.7116 (mtp) cc_final: 0.6740 (mtt) REVERT: C 380 GLN cc_start: 0.8255 (tt0) cc_final: 0.8004 (mt0) REVERT: C 392 ASN cc_start: 0.8301 (t0) cc_final: 0.7900 (t0) REVERT: D 176 THR cc_start: 0.7392 (p) cc_final: 0.6797 (t) REVERT: E 274 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7723 (tmtt) REVERT: E 303 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6571 (mm-30) REVERT: E 308 ASP cc_start: 0.7439 (t0) cc_final: 0.6735 (t0) REVERT: E 380 GLN cc_start: 0.8415 (tt0) cc_final: 0.8197 (tp-100) REVERT: F 135 THR cc_start: 0.8509 (p) cc_final: 0.7695 (p) REVERT: F 277 ASN cc_start: 0.7195 (m-40) cc_final: 0.6609 (m110) REVERT: F 313 ASN cc_start: 0.6645 (t0) cc_final: 0.5806 (t0) outliers start: 6 outliers final: 1 residues processed: 761 average time/residue: 0.1694 time to fit residues: 188.1230 Evaluate side-chains 408 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 405 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.0670 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 229 HIS A 348 HIS A 393 HIS A 408 GLN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS B 245 HIS B 251 ASN B 329 ASN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS C 229 HIS C 247 ASN C 414 ASN E 34 GLN E 196 ASN F 27 HIS F 78 GLN ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.140232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.123896 restraints weight = 43174.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.126408 restraints weight = 26399.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.128198 restraints weight = 18158.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.129463 restraints weight = 13489.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.130212 restraints weight = 10709.334| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4014 r_free = 0.4014 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4014 r_free = 0.4014 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19990 Z= 0.134 Angle : 0.625 8.203 26950 Z= 0.310 Chirality : 0.044 0.177 3170 Planarity : 0.004 0.095 3434 Dihedral : 9.583 167.113 2788 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: -1.32 (0.14), residues: 2512 helix: -1.07 (0.14), residues: 1040 sheet: 0.05 (0.20), residues: 456 loop : -0.90 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 416 TYR 0.014 0.001 TYR B 401 PHE 0.016 0.001 PHE D 224 TRP 0.006 0.001 TRP B 283 HIS 0.014 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (19990) covalent geometry : angle 0.62483 / 0.31 (26950) hydrogen bonds : bond 0.03854 / 2.58 ( 832) hydrogen bonds : angle 5.85246 / 4.02 ( 2382) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ARG cc_start: 0.7448 (mpt180) cc_final: 0.7191 (mtp180) REVERT: A 215 LEU cc_start: 0.7078 (mt) cc_final: 0.6567 (mt) REVERT: A 259 MET cc_start: 0.2409 (mtt) cc_final: 0.1937 (mtm) REVERT: A 260 MET cc_start: 0.6458 (ptm) cc_final: 0.5870 (ppp) REVERT: B 46 MET cc_start: 0.8506 (mmm) cc_final: 0.8021 (mmm) REVERT: B 60 LEU cc_start: 0.8121 (tp) cc_final: 0.7397 (pp) REVERT: B 117 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7417 (tm-30) REVERT: B 174 LEU cc_start: 0.6840 (mt) cc_final: 0.6514 (mt) REVERT: B 443 MET cc_start: 0.7428 (mmp) cc_final: 0.6921 (ppp) REVERT: C 28 GLU cc_start: 0.7495 (tp30) cc_final: 0.7192 (tp30) REVERT: C 110 GLU cc_start: 0.7917 (tp30) cc_final: 0.7658 (tp30) REVERT: C 271 ILE cc_start: 0.8427 (mm) cc_final: 0.8086 (mm) REVERT: C 341 THR cc_start: 0.8071 (p) cc_final: 0.7781 (t) REVERT: C 359 MET cc_start: 0.6574 (mtp) cc_final: 0.6347 (mtp) REVERT: D 94 LEU cc_start: 0.9003 (tp) cc_final: 0.8784 (mt) REVERT: D 176 THR cc_start: 0.7035 (p) cc_final: 0.6682 (t) REVERT: E 308 ASP cc_start: 0.7093 (t0) cc_final: 0.6526 (t0) REVERT: F 313 ASN cc_start: 0.6657 (t0) cc_final: 0.5750 (t0) REVERT: F 368 LYS cc_start: 0.7896 (tttt) cc_final: 0.7387 (tttt) outliers start: 0 outliers final: 0 residues processed: 472 average time/residue: 0.1565 time to fit residues: 110.3270 Evaluate side-chains 319 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 152 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 154 optimal weight: 0.0870 chunk 201 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 0.0770 chunk 230 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 chunk 134 optimal weight: 6.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN B 341 GLN C 229 HIS C 247 ASN C 414 ASN D 146 GLN E 305 HIS F 27 HIS F 245 HIS F 277 ASN F 404 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.140044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.123739 restraints weight = 43553.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.126310 restraints weight = 26630.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.128072 restraints weight = 18186.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.129289 restraints weight = 13559.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.130153 restraints weight = 10840.338| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4018 r_free = 0.4018 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4018 r_free = 0.4018 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19990 Z= 0.111 Angle : 0.599 7.407 26950 Z= 0.292 Chirality : 0.043 0.164 3170 Planarity : 0.004 0.057 3434 Dihedral : 9.286 167.194 2788 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.59 % Favored : 97.37 % Rotamer: Outliers : 0.05 % Allowed : 2.24 % Favored : 97.71 % 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: -0.69 (0.15), residues: 2512 helix: -0.38 (0.15), residues: 1052 sheet: 0.42 (0.22), residues: 458 loop : -0.80 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 130 TYR 0.019 0.001 TYR B 401 PHE 0.022 0.001 PHE D 224 TRP 0.019 0.002 TRP B 283 HIS 0.013 0.001 HIS F 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (19990) covalent geometry : angle 0.59910 / 0.29 (26950) hydrogen bonds : bond 0.03440 / 2.30 ( 832) hydrogen bonds : angle 5.23197 / 3.61 ( 2382) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 436 time to evaluate : 0.760 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: A 184 ARG cc_start: 0.7505 (mpt180) cc_final: 0.7196 (mtp180) REVERT: A 215 LEU cc_start: 0.6826 (mt) cc_final: 0.6511 (mt) REVERT: A 259 MET cc_start: 0.2893 (mtt) cc_final: 0.2609 (mtm) REVERT: A 260 MET cc_start: 0.6504 (ptm) cc_final: 0.5985 (ppp) REVERT: B 174 LEU cc_start: 0.6728 (mt) cc_final: 0.6497 (mt) REVERT: B 443 MET cc_start: 0.7353 (mmp) cc_final: 0.6795 (ppp) REVERT: C 28 GLU cc_start: 0.7434 (tp30) cc_final: 0.7127 (tp30) REVERT: C 110 GLU cc_start: 0.7792 (tp30) cc_final: 0.7554 (tp30) REVERT: C 115 ASN cc_start: 0.7752 (m-40) cc_final: 0.7376 (m110) REVERT: C 302 ASP cc_start: 0.7065 (t0) cc_final: 0.6816 (t0) REVERT: C 341 THR cc_start: 0.7891 (p) cc_final: 0.7666 (t) REVERT: C 359 MET cc_start: 0.6763 (mtp) cc_final: 0.6486 (mtp) REVERT: C 376 LYS cc_start: 0.8449 (tptt) cc_final: 0.8217 (tppt) REVERT: D 94 LEU cc_start: 0.8982 (tp) cc_final: 0.8776 (mt) REVERT: D 176 THR cc_start: 0.7181 (p) cc_final: 0.6758 (t) REVERT: D 191 ASP cc_start: 0.6409 (m-30) cc_final: 0.6185 (m-30) REVERT: D 223 LYS cc_start: 0.7458 (mptt) cc_final: 0.6481 (tttp) REVERT: D 254 THR cc_start: 0.7783 (p) cc_final: 0.7516 (p) REVERT: D 314 ARG cc_start: 0.7418 (mmt180) cc_final: 0.7154 (mmt90) REVERT: E 100 GLU cc_start: 0.8347 (mp0) cc_final: 0.7496 (mp0) REVERT: E 308 ASP cc_start: 0.7257 (t0) cc_final: 0.6971 (t0) REVERT: F 311 PHE cc_start: 0.7338 (t80) cc_final: 0.7101 (t80) REVERT: F 314 ARG cc_start: 0.6479 (ptp-110) cc_final: 0.6120 (ttm-80) REVERT: F 352 ASP cc_start: 0.7507 (m-30) cc_final: 0.7249 (p0) outliers start: 1 outliers final: 0 residues processed: 437 average time/residue: 0.1437 time to fit residues: 96.1755 Evaluate side-chains 311 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 28 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 213 optimal weight: 0.4980 chunk 32 optimal weight: 0.2980 chunk 169 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 203 GLN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 HIS C 229 HIS C 247 ASN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.134859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.118731 restraints weight = 44478.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.121147 restraints weight = 27153.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.122828 restraints weight = 18626.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.123853 restraints weight = 13996.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.124709 restraints weight = 11446.996| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19990 Z= 0.139 Angle : 0.626 9.606 26950 Z= 0.309 Chirality : 0.044 0.160 3170 Planarity : 0.004 0.033 3434 Dihedral : 9.141 161.416 2788 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -0.41 (0.16), residues: 2512 helix: -0.04 (0.15), residues: 1052 sheet: 0.48 (0.23), residues: 457 loop : -0.74 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 235 TYR 0.022 0.002 TYR B 401 PHE 0.021 0.002 PHE D 309 TRP 0.013 0.001 TRP B 283 HIS 0.007 0.001 HIS E 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (19990) covalent geometry : angle 0.62566 / 0.31 (26950) hydrogen bonds : bond 0.03511 / 2.34 ( 832) hydrogen bonds : angle 4.96225 / 3.42 ( 2382) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.856 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: A 184 ARG cc_start: 0.7666 (mpt180) cc_final: 0.7254 (mtp180) REVERT: A 215 LEU cc_start: 0.7056 (mt) cc_final: 0.6769 (mt) REVERT: A 259 MET cc_start: 0.3677 (mtt) cc_final: 0.3280 (mtm) REVERT: A 260 MET cc_start: 0.6669 (ptm) cc_final: 0.6107 (ppp) REVERT: B 174 LEU cc_start: 0.6924 (mt) cc_final: 0.6547 (mt) REVERT: B 443 MET cc_start: 0.7257 (mmp) cc_final: 0.6735 (ppp) REVERT: C 302 ASP cc_start: 0.7449 (t0) cc_final: 0.7237 (t0) REVERT: C 341 THR cc_start: 0.8016 (p) cc_final: 0.7719 (t) REVERT: C 359 MET cc_start: 0.6841 (mtp) cc_final: 0.6625 (mtp) REVERT: D 191 ASP cc_start: 0.6606 (m-30) cc_final: 0.6384 (m-30) REVERT: D 314 ARG cc_start: 0.7506 (mmt180) cc_final: 0.7202 (mmt90) REVERT: E 100 GLU cc_start: 0.8524 (mp0) cc_final: 0.7620 (mp0) REVERT: E 308 ASP cc_start: 0.7413 (t0) cc_final: 0.6773 (t0) REVERT: F 311 PHE cc_start: 0.7505 (t80) cc_final: 0.7054 (t80) REVERT: F 314 ARG cc_start: 0.6595 (ptp-110) cc_final: 0.6359 (ttm-80) REVERT: F 352 ASP cc_start: 0.7622 (m-30) cc_final: 0.7366 (p0) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.1457 time to fit residues: 88.7402 Evaluate side-chains 290 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 88 optimal weight: 0.7980 chunk 250 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 234 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS C 247 ASN C 414 ASN F 27 HIS F 344 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.135063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.119125 restraints weight = 44020.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.121560 restraints weight = 26770.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.123257 restraints weight = 18316.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.124430 restraints weight = 13689.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.125151 restraints weight = 10985.239| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19990 Z= 0.119 Angle : 0.612 8.869 26950 Z= 0.298 Chirality : 0.044 0.168 3170 Planarity : 0.003 0.060 3434 Dihedral : 8.915 160.045 2788 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: -0.20 (0.16), residues: 2512 helix: 0.24 (0.16), residues: 1019 sheet: 0.49 (0.23), residues: 445 loop : -0.66 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 29 TYR 0.022 0.001 TYR B 401 PHE 0.020 0.002 PHE A 116 TRP 0.012 0.001 TRP B 283 HIS 0.005 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (19990) covalent geometry : angle 0.61165 / 0.30 (26950) hydrogen bonds : bond 0.03359 / 2.25 ( 832) hydrogen bonds : angle 4.84110 / 3.33 ( 2382) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.832 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: A 105 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 203 GLN cc_start: 0.6387 (tp40) cc_final: 0.5970 (tp40) REVERT: A 215 LEU cc_start: 0.7068 (mt) cc_final: 0.6826 (mt) REVERT: A 259 MET cc_start: 0.4122 (mtt) cc_final: 0.3615 (mtm) REVERT: A 260 MET cc_start: 0.6640 (ptm) cc_final: 0.6118 (ppp) REVERT: A 316 HIS cc_start: 0.7729 (p90) cc_final: 0.7316 (p90) REVERT: B 174 LEU cc_start: 0.6882 (mt) cc_final: 0.6543 (mt) REVERT: B 326 MET cc_start: 0.7876 (mpp) cc_final: 0.7547 (mpp) REVERT: B 375 CYS cc_start: 0.5816 (m) cc_final: 0.2427 (m) REVERT: C 28 GLU cc_start: 0.7520 (tp30) cc_final: 0.7239 (tp30) REVERT: C 264 MET cc_start: 0.3671 (ppp) cc_final: 0.3427 (ppp) REVERT: C 341 THR cc_start: 0.8045 (p) cc_final: 0.7817 (t) REVERT: D 94 LEU cc_start: 0.8982 (tp) cc_final: 0.8736 (mt) REVERT: D 314 ARG cc_start: 0.7482 (mmt180) cc_final: 0.7061 (mmt180) REVERT: E 308 ASP cc_start: 0.7155 (t0) cc_final: 0.6952 (t0) REVERT: F 311 PHE cc_start: 0.7526 (t80) cc_final: 0.7002 (t80) REVERT: F 314 ARG cc_start: 0.6496 (ptp-110) cc_final: 0.6026 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.1432 time to fit residues: 87.0354 Evaluate side-chains 285 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 172 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 239 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 215 optimal weight: 0.3980 chunk 192 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS C 247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.135275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.119275 restraints weight = 43847.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.121693 restraints weight = 26800.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.123374 restraints weight = 18442.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.124415 restraints weight = 13898.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.125279 restraints weight = 11338.045| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19990 Z= 0.113 Angle : 0.616 10.699 26950 Z= 0.299 Chirality : 0.044 0.171 3170 Planarity : 0.003 0.045 3434 Dihedral : 8.611 158.483 2788 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: -0.14 (0.16), residues: 2512 helix: 0.31 (0.16), residues: 1040 sheet: 0.47 (0.23), residues: 455 loop : -0.66 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.025 0.002 TYR B 401 PHE 0.016 0.001 PHE D 309 TRP 0.018 0.002 TRP B 283 HIS 0.006 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (19990) covalent geometry : angle 0.61626 / 0.30 (26950) hydrogen bonds : bond 0.03306 / 2.21 ( 832) hydrogen bonds : angle 4.75616 / 3.29 ( 2382) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.865 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: A 105 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7201 (mt-10) REVERT: A 203 GLN cc_start: 0.6553 (tp40) cc_final: 0.6086 (tp40) REVERT: A 259 MET cc_start: 0.3995 (mtt) cc_final: 0.3574 (mtm) REVERT: A 260 MET cc_start: 0.6721 (ptm) cc_final: 0.6223 (ppp) REVERT: A 316 HIS cc_start: 0.7747 (p90) cc_final: 0.7409 (p90) REVERT: B 174 LEU cc_start: 0.6904 (mt) cc_final: 0.6657 (mt) REVERT: B 375 CYS cc_start: 0.6011 (m) cc_final: 0.5811 (m) REVERT: C 302 ASP cc_start: 0.7296 (t0) cc_final: 0.6921 (t0) REVERT: C 341 THR cc_start: 0.8040 (p) cc_final: 0.7798 (t) REVERT: D 167 GLU cc_start: 0.8453 (tp30) cc_final: 0.7583 (pm20) REVERT: E 259 MET cc_start: 0.6809 (mpp) cc_final: 0.6505 (mpp) REVERT: E 308 ASP cc_start: 0.7105 (t0) cc_final: 0.6828 (t0) REVERT: F 311 PHE cc_start: 0.7526 (t80) cc_final: 0.7103 (t80) REVERT: F 314 ARG cc_start: 0.6486 (ptp-110) cc_final: 0.6065 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.1314 time to fit residues: 80.5167 Evaluate side-chains 283 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 67 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 158 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN C 229 HIS C 247 ASN ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 HIS D 344 HIS E 229 HIS E 305 HIS E 380 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.127387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.111342 restraints weight = 45133.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.113693 restraints weight = 27352.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.115289 restraints weight = 18734.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.116421 restraints weight = 14094.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.117101 restraints weight = 11345.786| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.6060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19990 Z= 0.183 Angle : 0.703 11.659 26950 Z= 0.348 Chirality : 0.046 0.174 3170 Planarity : 0.004 0.042 3434 Dihedral : 8.669 166.179 2788 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.18 % Favored : 95.78 % Rotamer: Outliers : 0.05 % Allowed : 1.82 % Favored : 98.13 % 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: -0.46 (0.16), residues: 2512 helix: 0.11 (0.15), residues: 1040 sheet: 0.17 (0.23), residues: 467 loop : -0.84 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 29 TYR 0.030 0.002 TYR B 401 PHE 0.038 0.002 PHE A 116 TRP 0.012 0.002 TRP B 283 HIS 0.008 0.002 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (19990) covalent geometry : angle 0.70252 / 0.35 (26950) hydrogen bonds : bond 0.03970 / 2.66 ( 832) hydrogen bonds : angle 5.04408 / 3.47 ( 2382) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7358 (mt-10) REVERT: A 203 GLN cc_start: 0.6321 (tp40) cc_final: 0.5962 (tp40) REVERT: A 259 MET cc_start: 0.4025 (mtt) cc_final: 0.3634 (mtt) REVERT: A 260 MET cc_start: 0.6811 (ptm) cc_final: 0.6447 (ppp) REVERT: B 174 LEU cc_start: 0.7218 (mt) cc_final: 0.6862 (mt) REVERT: C 110 GLU cc_start: 0.7772 (tp30) cc_final: 0.7519 (tp30) REVERT: C 264 MET cc_start: 0.3694 (ppp) cc_final: 0.3256 (ppp) REVERT: C 341 THR cc_start: 0.8375 (p) cc_final: 0.8102 (t) REVERT: E 308 ASP cc_start: 0.7407 (t0) cc_final: 0.7105 (t0) REVERT: F 88 MET cc_start: 0.7390 (mmp) cc_final: 0.7183 (mmt) REVERT: F 272 VAL cc_start: 0.8753 (t) cc_final: 0.8548 (p) REVERT: F 311 PHE cc_start: 0.7842 (t80) cc_final: 0.7451 (t80) REVERT: F 314 ARG cc_start: 0.6529 (ptp-110) cc_final: 0.6097 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.1276 time to fit residues: 72.4497 Evaluate side-chains 278 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 116 optimal weight: 0.0870 chunk 243 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 chunk 206 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN C 18 HIS C 229 HIS ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.125191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.109414 restraints weight = 45725.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.111714 restraints weight = 27721.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.113284 restraints weight = 18998.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.114390 restraints weight = 14273.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.115128 restraints weight = 11510.052| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19990 Z= 0.192 Angle : 0.727 13.273 26950 Z= 0.362 Chirality : 0.047 0.236 3170 Planarity : 0.004 0.040 3434 Dihedral : 8.649 176.658 2788 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.86 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -0.64 (0.16), residues: 2512 helix: 0.02 (0.16), residues: 1043 sheet: 0.06 (0.23), residues: 462 loop : -1.00 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 149 TYR 0.022 0.002 TYR D 172 PHE 0.031 0.002 PHE A 116 TRP 0.009 0.002 TRP B 283 HIS 0.007 0.002 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (19990) covalent geometry : angle 0.72718 / 0.36 (26950) hydrogen bonds : bond 0.04153 / 2.80 ( 832) hydrogen bonds : angle 5.15024 / 3.56 ( 2382) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7385 (mt-10) REVERT: A 203 GLN cc_start: 0.6512 (tp40) cc_final: 0.6071 (tp40) REVERT: A 259 MET cc_start: 0.3678 (mtt) cc_final: 0.3386 (mtt) REVERT: A 260 MET cc_start: 0.6847 (ptm) cc_final: 0.6564 (ppp) REVERT: A 316 HIS cc_start: 0.8233 (p90) cc_final: 0.7904 (p90) REVERT: B 174 LEU cc_start: 0.7308 (mt) cc_final: 0.7030 (mt) REVERT: C 264 MET cc_start: 0.3893 (ppp) cc_final: 0.3404 (ppp) REVERT: C 341 THR cc_start: 0.8477 (p) cc_final: 0.8155 (t) REVERT: C 359 MET cc_start: 0.6643 (mtt) cc_final: 0.6054 (mtt) REVERT: D 303 MET cc_start: 0.8233 (tpp) cc_final: 0.7934 (tpp) REVERT: F 311 PHE cc_start: 0.7794 (t80) cc_final: 0.7462 (t80) REVERT: F 314 ARG cc_start: 0.6607 (ptp-110) cc_final: 0.6133 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.1307 time to fit residues: 70.7039 Evaluate side-chains 268 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 87 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 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 = 0.3966 r_free = 0.3966 target = 0.126118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.110401 restraints weight = 45094.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.112827 restraints weight = 26895.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.114390 restraints weight = 18138.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.115544 restraints weight = 13557.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.116366 restraints weight = 10852.144| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.6706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19990 Z= 0.157 Angle : 0.688 11.897 26950 Z= 0.340 Chirality : 0.046 0.190 3170 Planarity : 0.004 0.050 3434 Dihedral : 8.422 174.020 2788 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.62 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -0.61 (0.16), residues: 2512 helix: 0.06 (0.16), residues: 1042 sheet: 0.08 (0.23), residues: 461 loop : -1.02 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 29 TYR 0.021 0.002 TYR B 401 PHE 0.026 0.002 PHE A 116 TRP 0.014 0.002 TRP B 283 HIS 0.006 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (19990) covalent geometry : angle 0.68815 / 0.34 (26950) hydrogen bonds : bond 0.03932 / 2.64 ( 832) hydrogen bonds : angle 5.04543 / 3.48 ( 2382) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7177 (mt-10) REVERT: A 180 LEU cc_start: 0.7980 (tp) cc_final: 0.7336 (mm) REVERT: A 203 GLN cc_start: 0.6411 (tp40) cc_final: 0.5799 (tp40) REVERT: A 259 MET cc_start: 0.3444 (mtt) cc_final: 0.3111 (mtt) REVERT: A 260 MET cc_start: 0.6832 (ptm) cc_final: 0.6599 (ppp) REVERT: B 174 LEU cc_start: 0.7494 (mt) cc_final: 0.7108 (mt) REVERT: C 110 GLU cc_start: 0.7584 (tp30) cc_final: 0.7143 (tp30) REVERT: C 264 MET cc_start: 0.3725 (ppp) cc_final: 0.3520 (ppp) REVERT: C 341 THR cc_start: 0.8509 (p) cc_final: 0.8165 (t) REVERT: C 359 MET cc_start: 0.6590 (mtt) cc_final: 0.6003 (mtt) REVERT: C 415 LEU cc_start: 0.8818 (mm) cc_final: 0.8545 (mt) REVERT: E 21 VAL cc_start: 0.7133 (p) cc_final: 0.6930 (p) REVERT: F 246 GLU cc_start: 0.8873 (pm20) cc_final: 0.8642 (pm20) REVERT: F 311 PHE cc_start: 0.7834 (t80) cc_final: 0.7415 (t80) REVERT: F 314 ARG cc_start: 0.6494 (ptp-110) cc_final: 0.6130 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.1351 time to fit residues: 72.5514 Evaluate side-chains 277 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 180 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.127448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.111786 restraints weight = 44918.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.114235 restraints weight = 26667.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.115897 restraints weight = 17870.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.117033 restraints weight = 13213.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.117771 restraints weight = 10568.047| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.6786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19990 Z= 0.136 Angle : 0.670 10.746 26950 Z= 0.330 Chirality : 0.046 0.195 3170 Planarity : 0.004 0.038 3434 Dihedral : 8.251 164.267 2788 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.98 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -0.54 (0.16), residues: 2512 helix: 0.13 (0.16), residues: 1044 sheet: 0.09 (0.24), residues: 449 loop : -0.96 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 29 TYR 0.031 0.002 TYR B 401 PHE 0.022 0.002 PHE A 116 TRP 0.015 0.002 TRP B 283 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (19990) covalent geometry : angle 0.67015 / 0.33 (26950) hydrogen bonds : bond 0.03731 / 2.50 ( 832) hydrogen bonds : angle 4.93990 / 3.41 ( 2382) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6972 (mt-10) REVERT: A 203 GLN cc_start: 0.6265 (tp40) cc_final: 0.5674 (tp40) REVERT: A 259 MET cc_start: 0.3296 (mtt) cc_final: 0.2904 (mtt) REVERT: A 260 MET cc_start: 0.6842 (ptm) cc_final: 0.6611 (ppp) REVERT: B 174 LEU cc_start: 0.7572 (mt) cc_final: 0.7282 (mt) REVERT: C 110 GLU cc_start: 0.7621 (tp30) cc_final: 0.7074 (tp30) REVERT: C 264 MET cc_start: 0.3906 (ppp) cc_final: 0.3568 (ppp) REVERT: C 341 THR cc_start: 0.8373 (p) cc_final: 0.8028 (t) REVERT: C 359 MET cc_start: 0.6546 (mtt) cc_final: 0.6081 (mtt) REVERT: D 90 MET cc_start: 0.7966 (ttt) cc_final: 0.7742 (ttm) REVERT: D 338 THR cc_start: 0.8838 (t) cc_final: 0.8619 (m) REVERT: F 246 GLU cc_start: 0.8820 (pm20) cc_final: 0.8585 (pm20) REVERT: F 311 PHE cc_start: 0.7896 (t80) cc_final: 0.7485 (t80) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1319 time to fit residues: 71.0622 Evaluate side-chains 277 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 121 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 60 optimal weight: 0.4980 chunk 160 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.125966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.110620 restraints weight = 45359.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.112887 restraints weight = 27366.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.114437 restraints weight = 18606.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.115416 restraints weight = 13987.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.116261 restraints weight = 11383.994| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.6937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19990 Z= 0.154 Angle : 0.687 11.057 26950 Z= 0.339 Chirality : 0.046 0.186 3170 Planarity : 0.004 0.046 3434 Dihedral : 8.217 152.200 2788 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.21 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -0.64 (0.16), residues: 2512 helix: 0.06 (0.16), residues: 1050 sheet: 0.06 (0.23), residues: 462 loop : -1.06 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 29 TYR 0.040 0.002 TYR B 401 PHE 0.023 0.002 PHE A 116 TRP 0.011 0.001 TRP B 283 HIS 0.006 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (19990) covalent geometry : angle 0.68732 / 0.34 (26950) hydrogen bonds : bond 0.03807 / 2.56 ( 832) hydrogen bonds : angle 4.96787 / 3.44 ( 2382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3224.17 seconds wall clock time: 56 minutes 43.76 seconds (3403.76 seconds total)