Starting phenix.real_space_refine on Fri Feb 6 18:31:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ukm_64249/02_2026/9ukm_64249.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ukm_64249/02_2026/9ukm_64249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ukm_64249/02_2026/9ukm_64249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ukm_64249/02_2026/9ukm_64249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ukm_64249/02_2026/9ukm_64249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ukm_64249/02_2026/9ukm_64249.map" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.644 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: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 16981 2.51 5 N 4543 2.21 5 O 5113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26773 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3418 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 19, 'TRANS': 420} Chain: "B" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3418 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 19, 'TRANS': 420} Chain: "C" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3418 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 19, 'TRANS': 420} Chain: "D" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3418 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 19, 'TRANS': 420} Chain: "E" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3418 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 19, 'TRANS': 420} Chain: "F" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3418 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 19, 'TRANS': 420} Chain: "G" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3418 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 19, 'TRANS': 420} Chain: "H" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 555 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "I" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2292 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 6, 'TRANS': 296} Chain breaks: 1 Time building chain proxies: 6.36, per 1000 atoms: 0.24 Number of scatterers: 26773 At special positions: 0 Unit cell: (242.08, 303.28, 155.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 5113 8.00 N 4543 7.00 C 16981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6416 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 47 sheets defined 26.2% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.677A pdb=" N SER A 130 " --> pdb=" O MET A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.606A pdb=" N PHE A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 345 through 373 removed outlier: 3.730A pdb=" N LEU A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 413 removed outlier: 3.892A pdb=" N TRP A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 432 removed outlier: 3.671A pdb=" N GLN A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 536 through 539 Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 345 through 374 removed outlier: 3.584A pdb=" N LEU B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B 374 " --> pdb=" O MET B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 413 removed outlier: 3.829A pdb=" N TRP B 393 " --> pdb=" O SER B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 432 Processing helix chain 'B' and resid 466 through 476 Processing helix chain 'B' and resid 536 through 539 Processing helix chain 'C' and resid 220 through 224 Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 345 through 373 removed outlier: 3.607A pdb=" N LEU C 349 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 367 " --> pdb=" O ASP C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 413 removed outlier: 3.602A pdb=" N TRP C 393 " --> pdb=" O SER C 389 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 409 " --> pdb=" O TYR C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 431 Processing helix chain 'C' and resid 466 through 476 removed outlier: 3.676A pdb=" N GLU C 476 " --> pdb=" O ASN C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 539 No H-bonds generated for 'chain 'C' and resid 537 through 539' Processing helix chain 'D' and resid 129 through 133 removed outlier: 3.606A pdb=" N VAL D 133 " --> pdb=" O SER D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 Processing helix chain 'D' and resid 332 through 343 Processing helix chain 'D' and resid 345 through 373 removed outlier: 3.726A pdb=" N SER D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 413 removed outlier: 4.150A pdb=" N TRP D 393 " --> pdb=" O SER D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 431 Processing helix chain 'D' and resid 466 through 476 Processing helix chain 'D' and resid 536 through 539 Processing helix chain 'E' and resid 152 through 156 removed outlier: 3.564A pdb=" N ALA E 155 " --> pdb=" O THR E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 332 through 343 Processing helix chain 'E' and resid 345 through 374 removed outlier: 3.876A pdb=" N SER E 359 " --> pdb=" O LYS E 355 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN E 362 " --> pdb=" O LEU E 358 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU E 367 " --> pdb=" O ASP E 363 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR E 374 " --> pdb=" O MET E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 413 removed outlier: 3.647A pdb=" N TRP E 393 " --> pdb=" O SER E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 432 Processing helix chain 'E' and resid 466 through 476 Processing helix chain 'E' and resid 537 through 541 removed outlier: 3.672A pdb=" N TYR E 540 " --> pdb=" O GLY E 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 250 No H-bonds generated for 'chain 'F' and resid 248 through 250' Processing helix chain 'F' and resid 331 through 342 Processing helix chain 'F' and resid 345 through 374 removed outlier: 3.631A pdb=" N LEU F 367 " --> pdb=" O ASP F 363 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR F 374 " --> pdb=" O MET F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 413 removed outlier: 3.871A pdb=" N TRP F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 431 Processing helix chain 'F' and resid 466 through 476 Processing helix chain 'F' and resid 536 through 539 Processing helix chain 'G' and resid 129 through 133 Processing helix chain 'G' and resid 152 through 154 No H-bonds generated for 'chain 'G' and resid 152 through 154' Processing helix chain 'G' and resid 332 through 341 Processing helix chain 'G' and resid 345 through 374 removed outlier: 3.681A pdb=" N SER G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR G 374 " --> pdb=" O MET G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 413 removed outlier: 3.904A pdb=" N VAL G 404 " --> pdb=" O LYS G 400 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR G 405 " --> pdb=" O PHE G 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 423 through 433 removed outlier: 3.700A pdb=" N LEU G 433 " --> pdb=" O PHE G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 466 through 476 Processing helix chain 'G' and resid 536 through 539 Processing helix chain 'H' and resid 136 through 201 removed outlier: 3.935A pdb=" N VAL H 161 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER H 162 " --> pdb=" O GLN H 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 92 Processing helix chain 'I' and resid 139 through 141 No H-bonds generated for 'chain 'I' and resid 139 through 141' Processing helix chain 'I' and resid 175 through 180 Processing helix chain 'I' and resid 188 through 236 removed outlier: 3.604A pdb=" N VAL I 192 " --> pdb=" O THR I 188 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA I 205 " --> pdb=" O GLU I 201 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LYS I 206 " --> pdb=" O LYS I 202 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN I 211 " --> pdb=" O PHE I 207 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS I 212 " --> pdb=" O GLN I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 283 removed outlier: 4.258A pdb=" N THR I 283 " --> pdb=" O ARG I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 305 through 316 removed outlier: 3.631A pdb=" N ILE I 309 " --> pdb=" O ARG I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 356 through 374 removed outlier: 3.505A pdb=" N LYS I 372 " --> pdb=" O PHE I 368 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA I 373 " --> pdb=" O LYS I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 376 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 143 removed outlier: 7.726A pdb=" N TYR F 169 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N MET A 142 " --> pdb=" O TYR F 169 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL F 171 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER F 166 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU F 313 " --> pdb=" O PHE F 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 158 removed outlier: 5.950A pdb=" N THR A 157 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ASP A 503 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N THR A 501 " --> pdb=" O ASP A 531 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASP A 531 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ASP A 503 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 529 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA A 507 " --> pdb=" O TRP A 525 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TRP A 525 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR A 523 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLN A 511 " --> pdb=" O ARG A 521 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ARG A 521 " --> pdb=" O GLN A 511 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 310 through 314 removed outlier: 3.529A pdb=" N GLU A 313 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 166 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 310 through 314 removed outlier: 3.529A pdb=" N GLU A 313 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 200 through 206 removed outlier: 6.632A pdb=" N ILE A 292 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 215 through 218 removed outlier: 3.541A pdb=" N HIS A 255 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 253 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 381 removed outlier: 6.384A pdb=" N ASP A 378 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR A 547 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N PHE A 380 " --> pdb=" O THR A 547 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 490 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS A 461 " --> pdb=" O MET A 418 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY A 454 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU A 464 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR A 452 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 157 through 158 removed outlier: 5.773A pdb=" N THR B 157 " --> pdb=" O THR B 501 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ASP B 503 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR B 501 " --> pdb=" O ASP B 531 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASP B 531 " --> pdb=" O THR B 501 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP B 503 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE B 529 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA B 507 " --> pdb=" O TRP B 525 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TRP B 525 " --> pdb=" O ALA B 507 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR B 523 " --> pdb=" O PRO B 509 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLN B 511 " --> pdb=" O ARG B 521 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ARG B 521 " --> pdb=" O GLN B 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 187 removed outlier: 4.136A pdb=" N ASP B 186 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 166 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 310 through 314 removed outlier: 7.093A pdb=" N ASP B 167 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET C 142 " --> pdb=" O ASP B 167 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR B 169 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 200 through 206 removed outlier: 6.427A pdb=" N ILE B 292 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 215 through 219 Processing sheet with id=AB4, first strand: chain 'B' and resid 377 through 381 removed outlier: 6.266A pdb=" N ASP B 378 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N THR B 547 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 380 " --> pdb=" O THR B 547 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASP B 484 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 461 " --> pdb=" O MET B 418 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY B 454 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU B 464 " --> pdb=" O TYR B 452 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR B 452 " --> pdb=" O GLU B 464 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 158 removed outlier: 5.090A pdb=" N THR C 501 " --> pdb=" O ASP C 531 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ASP C 531 " --> pdb=" O THR C 501 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASP C 503 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 529 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA C 507 " --> pdb=" O TRP C 525 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TRP C 525 " --> pdb=" O ALA C 507 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR C 523 " --> pdb=" O PRO C 509 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLN C 511 " --> pdb=" O ARG C 521 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG C 521 " --> pdb=" O GLN C 511 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 310 through 319 removed outlier: 3.515A pdb=" N GLU C 170 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASP C 167 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ILE D 143 " --> pdb=" O ASP C 167 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TYR C 169 " --> pdb=" O ILE D 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 200 through 206 removed outlier: 6.686A pdb=" N ILE C 292 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 215 through 219 Processing sheet with id=AB9, first strand: chain 'C' and resid 376 through 381 removed outlier: 6.510A pdb=" N ALA C 376 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N THR C 545 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP C 378 " --> pdb=" O THR C 545 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR C 547 " --> pdb=" O ASP C 378 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE C 380 " --> pdb=" O THR C 547 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS C 461 " --> pdb=" O MET C 418 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL C 460 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR C 455 " --> pdb=" O VAL C 460 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL C 462 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 453 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS C 451 " --> pdb=" O GLU C 464 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 384 through 385 removed outlier: 3.619A pdb=" N LEU C 384 " --> pdb=" O LEU C 554 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP C 560 " --> pdb=" O ASN C 555 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 157 through 158 removed outlier: 5.532A pdb=" N THR D 157 " --> pdb=" O THR D 501 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASP D 503 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP D 531 " --> pdb=" O VAL D 500 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER D 527 " --> pdb=" O ALA D 504 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TRP D 525 " --> pdb=" O PRO D 506 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE D 508 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR D 523 " --> pdb=" O ILE D 508 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE D 510 " --> pdb=" O ARG D 521 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG D 521 " --> pdb=" O PHE D 510 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 314 through 319 removed outlier: 3.879A pdb=" N GLU D 170 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N GLN D 165 " --> pdb=" O PHE E 139 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N ALA E 141 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP D 167 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ILE E 143 " --> pdb=" O ASP D 167 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR D 169 " --> pdb=" O ILE E 143 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 174 through 175 Processing sheet with id=AC5, first strand: chain 'D' and resid 200 through 206 removed outlier: 6.629A pdb=" N ILE D 292 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 215 through 219 removed outlier: 3.804A pdb=" N LEU D 253 " --> pdb=" O CYS D 269 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 377 through 381 removed outlier: 6.911A pdb=" N ASP D 378 " --> pdb=" O THR D 545 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR D 547 " --> pdb=" O ASP D 378 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE D 380 " --> pdb=" O THR D 547 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP D 484 " --> pdb=" O GLY D 423 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N MET D 420 " --> pdb=" O TYR D 463 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL D 465 " --> pdb=" O MET D 420 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA D 422 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY D 454 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU D 464 " --> pdb=" O TYR D 452 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR D 452 " --> pdb=" O GLU D 464 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR D 455 " --> pdb=" O GLN D 439 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 384 through 385 removed outlier: 4.182A pdb=" N LEU D 384 " --> pdb=" O LEU D 554 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 157 through 158 removed outlier: 7.962A pdb=" N GLY E 502 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASP E 531 " --> pdb=" O GLY E 502 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA E 504 " --> pdb=" O ILE E 529 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE E 529 " --> pdb=" O ALA E 504 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N SER E 527 " --> pdb=" O PRO E 506 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG E 521 " --> pdb=" O HIS E 512 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 310 through 319 removed outlier: 3.622A pdb=" N GLU E 313 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP E 167 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET F 142 " --> pdb=" O ASP E 167 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR E 169 " --> pdb=" O MET F 142 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 200 through 206 removed outlier: 6.686A pdb=" N ILE E 292 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU E 297 " --> pdb=" O ARG E 234 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ARG E 234 " --> pdb=" O GLU E 297 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 215 through 219 Processing sheet with id=AD4, first strand: chain 'E' and resid 377 through 381 removed outlier: 6.610A pdb=" N ASP E 378 " --> pdb=" O THR E 545 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N THR E 547 " --> pdb=" O ASP E 378 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N PHE E 380 " --> pdb=" O THR E 547 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP E 484 " --> pdb=" O GLY E 423 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS E 461 " --> pdb=" O MET E 418 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY E 454 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU E 464 " --> pdb=" O TYR E 452 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR E 452 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 384 through 385 removed outlier: 4.299A pdb=" N LEU E 384 " --> pdb=" O LEU E 554 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP E 560 " --> pdb=" O ASN E 555 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 157 through 158 removed outlier: 5.736A pdb=" N THR F 157 " --> pdb=" O THR F 501 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ASP F 503 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N THR F 501 " --> pdb=" O ASP F 531 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASP F 531 " --> pdb=" O THR F 501 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASP F 503 " --> pdb=" O ILE F 529 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE F 529 " --> pdb=" O ASP F 503 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA F 507 " --> pdb=" O TRP F 525 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TRP F 525 " --> pdb=" O ALA F 507 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR F 523 " --> pdb=" O PRO F 509 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLN F 511 " --> pdb=" O ARG F 521 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ARG F 521 " --> pdb=" O GLN F 511 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL F 519 " --> pdb=" O PRO F 513 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY F 526 " --> pdb=" O PHE F 324 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 200 through 206 removed outlier: 7.066A pdb=" N ILE F 292 " --> pdb=" O LEU F 205 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 215 through 218 Processing sheet with id=AD9, first strand: chain 'F' and resid 377 through 381 removed outlier: 6.636A pdb=" N ASP F 378 " --> pdb=" O THR F 545 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR F 547 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE F 380 " --> pdb=" O THR F 547 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR F 488 " --> pdb=" O GLY F 419 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL F 460 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR F 455 " --> pdb=" O VAL F 460 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL F 462 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS F 451 " --> pdb=" O GLU F 464 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 384 through 385 removed outlier: 4.114A pdb=" N LEU F 384 " --> pdb=" O LEU F 554 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 156 through 158 removed outlier: 5.887A pdb=" N THR G 157 " --> pdb=" O THR G 501 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASP G 503 " --> pdb=" O THR G 157 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER G 527 " --> pdb=" O ALA G 504 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP G 525 " --> pdb=" O PRO G 506 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE G 508 " --> pdb=" O THR G 523 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR G 523 " --> pdb=" O ILE G 508 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE G 510 " --> pdb=" O ARG G 521 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG G 521 " --> pdb=" O PHE G 510 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 166 through 168 removed outlier: 3.707A pdb=" N SER G 166 " --> pdb=" O LEU G 319 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU G 319 " --> pdb=" O SER G 166 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 174 through 175 Processing sheet with id=AE5, first strand: chain 'G' and resid 200 through 206 removed outlier: 6.775A pdb=" N ILE G 292 " --> pdb=" O LEU G 205 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 215 through 219 removed outlier: 3.559A pdb=" N LEU G 253 " --> pdb=" O CYS G 269 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 377 through 381 removed outlier: 3.600A pdb=" N TYR G 488 " --> pdb=" O GLY G 419 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N LYS G 461 " --> pdb=" O GLY G 416 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N MET G 418 " --> pdb=" O LYS G 461 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N TYR G 463 " --> pdb=" O MET G 418 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N MET G 420 " --> pdb=" O TYR G 463 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY G 454 " --> pdb=" O VAL G 462 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU G 464 " --> pdb=" O TYR G 452 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR G 452 " --> pdb=" O GLU G 464 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 384 through 385 removed outlier: 3.529A pdb=" N LEU G 384 " --> pdb=" O LEU G 554 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 71 through 72 removed outlier: 5.359A pdb=" N ALA I 165 " --> pdb=" O HIS I 149 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS I 149 " --> pdb=" O ALA I 165 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN I 167 " --> pdb=" O LEU I 147 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 119 through 120 removed outlier: 3.842A pdb=" N GLN I 167 " --> pdb=" O LEU I 147 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS I 149 " --> pdb=" O ALA I 165 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ALA I 165 " --> pdb=" O HIS I 149 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 319 through 320 removed outlier: 4.113A pdb=" N MET I 327 " --> pdb=" O THR I 341 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY I 336 " --> pdb=" O ALA I 352 " (cutoff:3.500A) 1113 hydrogen bonds defined for protein. 3162 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: 5.51 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8861 1.34 - 1.46: 5869 1.46 - 1.58: 12333 1.58 - 1.70: 0 1.70 - 1.82: 244 Bond restraints: 27307 Sorted by residual: bond pdb=" N ILE I 136 " pdb=" CA ILE I 136 " ideal model delta sigma weight residual 1.458 1.494 -0.036 7.70e-03 1.69e+04 2.20e+01 bond pdb=" N HIS I 314 " pdb=" CA HIS I 314 " ideal model delta sigma weight residual 1.456 1.504 -0.047 1.33e-02 5.65e+03 1.27e+01 bond pdb=" N LEU I 138 " pdb=" CA LEU I 138 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.18e-02 7.18e+03 7.79e+00 bond pdb=" N ASP I 316 " pdb=" CA ASP I 316 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.21e-02 6.83e+03 7.76e+00 bond pdb=" N MET G 418 " pdb=" CA MET G 418 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.24e-02 6.50e+03 6.63e+00 ... (remaining 27302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 36548 2.25 - 4.49: 404 4.49 - 6.74: 42 6.74 - 8.99: 18 8.99 - 11.23: 3 Bond angle restraints: 37015 Sorted by residual: angle pdb=" CA GLU H 142 " pdb=" CB GLU H 142 " pdb=" CG GLU H 142 " ideal model delta sigma weight residual 114.10 123.56 -9.46 2.00e+00 2.50e-01 2.24e+01 angle pdb=" C ILE G 409 " pdb=" N GLU G 410 " pdb=" CA GLU G 410 " ideal model delta sigma weight residual 122.38 114.02 8.36 1.81e+00 3.05e-01 2.13e+01 angle pdb=" CA HIS I 314 " pdb=" C HIS I 314 " pdb=" N MET I 315 " ideal model delta sigma weight residual 118.21 112.58 5.63 1.36e+00 5.41e-01 1.71e+01 angle pdb=" CA GLN H 145 " pdb=" CB GLN H 145 " pdb=" CG GLN H 145 " ideal model delta sigma weight residual 114.10 122.09 -7.99 2.00e+00 2.50e-01 1.60e+01 angle pdb=" N PHE D 320 " pdb=" CA PHE D 320 " pdb=" C PHE D 320 " ideal model delta sigma weight residual 108.11 113.09 -4.98 1.29e+00 6.01e-01 1.49e+01 ... (remaining 37010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14750 17.95 - 35.90: 1360 35.90 - 53.85: 216 53.85 - 71.80: 27 71.80 - 89.75: 15 Dihedral angle restraints: 16368 sinusoidal: 6392 harmonic: 9976 Sorted by residual: dihedral pdb=" CA MET I 235 " pdb=" C MET I 235 " pdb=" N SER I 236 " pdb=" CA SER I 236 " ideal model delta harmonic sigma weight residual -180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA SER I 236 " pdb=" C SER I 236 " pdb=" N ASP I 237 " pdb=" CA ASP I 237 " ideal model delta harmonic sigma weight residual -180.00 -158.67 -21.33 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA HIS F 330 " pdb=" C HIS F 330 " pdb=" N THR F 331 " pdb=" CA THR F 331 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 16365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3283 0.046 - 0.092: 610 0.092 - 0.139: 293 0.139 - 0.185: 7 0.185 - 0.231: 2 Chirality restraints: 4195 Sorted by residual: chirality pdb=" CA GLU H 142 " pdb=" N GLU H 142 " pdb=" C GLU H 142 " pdb=" CB GLU H 142 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ILE I 136 " pdb=" N ILE I 136 " pdb=" C ILE I 136 " pdb=" CB ILE I 136 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA GLN H 167 " pdb=" N GLN H 167 " pdb=" C GLN H 167 " pdb=" CB GLN H 167 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 ... (remaining 4192 not shown) Planarity restraints: 4819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU H 142 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" CD GLU H 142 " 0.049 2.00e-02 2.50e+03 pdb=" OE1 GLU H 142 " -0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU H 142 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 535 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C ARG D 535 " -0.039 2.00e-02 2.50e+03 pdb=" O ARG D 535 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN D 536 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG I 312 " 0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C ARG I 312 " -0.035 2.00e-02 2.50e+03 pdb=" O ARG I 312 " 0.013 2.00e-02 2.50e+03 pdb=" N MET I 313 " 0.012 2.00e-02 2.50e+03 ... (remaining 4816 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2594 2.74 - 3.28: 26813 3.28 - 3.82: 42589 3.82 - 4.36: 47357 4.36 - 4.90: 84491 Nonbonded interactions: 203844 Sorted by model distance: nonbonded pdb=" O ASN A 477 " pdb=" ND2 ASN A 477 " model vdw 2.200 3.120 nonbonded pdb=" OG SER F 209 " pdb=" OG1 THR F 290 " model vdw 2.213 3.040 nonbonded pdb=" OG SER A 209 " pdb=" OG1 THR A 290 " model vdw 2.214 3.040 nonbonded pdb=" N GLU D 492 " pdb=" OE1 GLU D 492 " model vdw 2.221 3.120 nonbonded pdb=" OH TYR E 405 " pdb=" O GLY E 419 " model vdw 2.221 3.040 ... (remaining 203839 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.680 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 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 : 0.004 0.049 27307 Z= 0.194 Angle : 0.612 11.233 37015 Z= 0.342 Chirality : 0.043 0.231 4195 Planarity : 0.004 0.040 4819 Dihedral : 13.826 89.747 9952 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.38 % Allowed : 11.93 % Favored : 87.69 % 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: -0.10 (0.14), residues: 3432 helix: 1.84 (0.18), residues: 856 sheet: 0.15 (0.17), residues: 929 loop : -1.25 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 373 TYR 0.018 0.001 TYR F 357 PHE 0.024 0.001 PHE I 207 TRP 0.012 0.001 TRP B 372 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00387 (27307) covalent geometry : angle 0.61239 (37015) hydrogen bonds : bond 0.20262 ( 1101) hydrogen bonds : angle 7.79715 ( 3162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 92 LEU cc_start: 0.7571 (mp) cc_final: 0.7324 (mp) outliers start: 11 outliers final: 2 residues processed: 217 average time/residue: 0.1837 time to fit residues: 63.0358 Evaluate side-chains 210 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 208 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain I residue 371 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 0.0970 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN C 432 GLN D 240 ASN D 362 GLN D 520 ASN F 312 HIS ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 ASN I 323 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.068188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.049511 restraints weight = 118411.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.050816 restraints weight = 50909.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.051661 restraints weight = 29107.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.052198 restraints weight = 19756.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.052536 restraints weight = 15215.902| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27307 Z= 0.121 Angle : 0.530 9.383 37015 Z= 0.287 Chirality : 0.044 0.168 4195 Planarity : 0.004 0.045 4819 Dihedral : 4.356 56.451 3727 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.42 % Allowed : 10.96 % Favored : 87.62 % 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: 0.12 (0.14), residues: 3432 helix: 2.04 (0.18), residues: 869 sheet: 0.27 (0.17), residues: 948 loop : -1.15 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 241 TYR 0.013 0.001 TYR A 488 PHE 0.018 0.001 PHE H 163 TRP 0.007 0.001 TRP B 372 HIS 0.003 0.001 HIS I 314 Details of bonding type rmsd covalent geometry : bond 0.00242 (27307) covalent geometry : angle 0.53011 (37015) hydrogen bonds : bond 0.05898 ( 1101) hydrogen bonds : angle 5.35356 ( 3162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.7138 (pmm) cc_final: 0.6936 (pmm) REVERT: A 220 MET cc_start: 0.9175 (tpp) cc_final: 0.8953 (tpp) REVERT: A 418 MET cc_start: 0.8757 (mmp) cc_final: 0.8211 (mmt) REVERT: D 142 MET cc_start: 0.8919 (tpp) cc_final: 0.8459 (tpt) REVERT: D 418 MET cc_start: 0.9095 (tpp) cc_final: 0.8033 (mmm) REVERT: E 314 MET cc_start: 0.7770 (ptt) cc_final: 0.7540 (ptm) REVERT: F 356 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: G 410 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8268 (pm20) REVERT: I 171 ASN cc_start: 0.9134 (t0) cc_final: 0.8765 (m-40) outliers start: 41 outliers final: 14 residues processed: 249 average time/residue: 0.1647 time to fit residues: 65.9632 Evaluate side-chains 227 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain C residue 548 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 269 CYS Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 418 MET Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain I residue 372 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 330 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 312 optimal weight: 5.9990 chunk 313 optimal weight: 10.0000 chunk 53 optimal weight: 0.0470 chunk 98 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 overall best weight: 3.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 GLN E 477 ASN H 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.066897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.048052 restraints weight = 118624.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.049340 restraints weight = 51387.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.050163 restraints weight = 29620.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.050703 restraints weight = 20170.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.051001 restraints weight = 15537.039| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 27307 Z= 0.169 Angle : 0.547 9.854 37015 Z= 0.292 Chirality : 0.043 0.174 4195 Planarity : 0.004 0.044 4819 Dihedral : 4.263 21.427 3723 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.70 % Allowed : 12.07 % Favored : 86.23 % 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: 0.10 (0.14), residues: 3432 helix: 1.95 (0.18), residues: 875 sheet: 0.26 (0.16), residues: 948 loop : -1.15 (0.14), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 368 TYR 0.013 0.001 TYR E 196 PHE 0.015 0.001 PHE D 401 TRP 0.008 0.001 TRP B 372 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00375 (27307) covalent geometry : angle 0.54704 (37015) hydrogen bonds : bond 0.06021 ( 1101) hydrogen bonds : angle 5.07384 ( 3162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.7178 (pmm) cc_final: 0.6936 (pmm) REVERT: A 220 MET cc_start: 0.9214 (tpp) cc_final: 0.8996 (tpp) REVERT: A 315 LYS cc_start: 0.7680 (mmtm) cc_final: 0.7455 (mmtm) REVERT: B 483 MET cc_start: 0.9137 (mmm) cc_final: 0.8432 (mmm) REVERT: C 134 MET cc_start: 0.8431 (mpp) cc_final: 0.8133 (pmm) REVERT: C 362 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: D 418 MET cc_start: 0.9197 (tpp) cc_final: 0.8054 (mmm) REVERT: F 220 MET cc_start: 0.9310 (mmm) cc_final: 0.9005 (mmm) REVERT: F 356 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8617 (mp0) REVERT: F 420 MET cc_start: 0.8640 (tpp) cc_final: 0.8268 (tpt) REVERT: F 442 GLU cc_start: 0.8401 (pp20) cc_final: 0.7809 (tm-30) REVERT: G 420 MET cc_start: 0.8896 (tpp) cc_final: 0.8227 (ttp) REVERT: H 191 GLU cc_start: 0.8534 (tp30) cc_final: 0.7819 (tm-30) REVERT: I 77 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7556 (mm) REVERT: I 79 ARG cc_start: 0.8966 (mpp80) cc_final: 0.8714 (mtt-85) REVERT: I 171 ASN cc_start: 0.9144 (t0) cc_final: 0.8713 (m-40) REVERT: I 316 ASP cc_start: 0.8580 (m-30) cc_final: 0.8157 (p0) REVERT: I 342 ASP cc_start: 0.7004 (t0) cc_final: 0.6685 (t0) outliers start: 49 outliers final: 24 residues processed: 251 average time/residue: 0.1768 time to fit residues: 70.9092 Evaluate side-chains 230 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 548 MET Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain E residue 269 CYS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 269 CYS Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 418 MET Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 372 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 186 optimal weight: 0.0370 chunk 108 optimal weight: 5.9990 chunk 297 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 289 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN C 388 GLN ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.067929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.049213 restraints weight = 117630.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050520 restraints weight = 50753.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.051356 restraints weight = 28979.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.051887 restraints weight = 19691.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.052226 restraints weight = 15144.404| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27307 Z= 0.117 Angle : 0.504 9.549 37015 Z= 0.270 Chirality : 0.043 0.181 4195 Planarity : 0.003 0.045 4819 Dihedral : 4.031 21.962 3723 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.80 % Allowed : 12.69 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3432 helix: 2.00 (0.18), residues: 874 sheet: 0.38 (0.16), residues: 962 loop : -1.10 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 490 TYR 0.011 0.001 TYR A 488 PHE 0.017 0.001 PHE H 163 TRP 0.007 0.001 TRP E 372 HIS 0.003 0.000 HIS I 314 Details of bonding type rmsd covalent geometry : bond 0.00242 (27307) covalent geometry : angle 0.50426 (37015) hydrogen bonds : bond 0.05338 ( 1101) hydrogen bonds : angle 4.71995 ( 3162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 219 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 134 MET cc_start: 0.7068 (pmm) cc_final: 0.6827 (pmm) REVERT: A 140 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9232 (mm) REVERT: A 220 MET cc_start: 0.9155 (tpp) cc_final: 0.8923 (tpp) REVERT: C 134 MET cc_start: 0.8427 (mpp) cc_final: 0.8118 (pmm) REVERT: C 362 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8399 (tm-30) REVERT: D 418 MET cc_start: 0.9094 (tpp) cc_final: 0.7898 (mmm) REVERT: F 195 VAL cc_start: 0.9602 (m) cc_final: 0.9349 (p) REVERT: F 220 MET cc_start: 0.9277 (mmm) cc_final: 0.9048 (mmm) REVERT: F 356 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8579 (mp0) REVERT: F 420 MET cc_start: 0.8590 (tpp) cc_final: 0.8043 (tpt) REVERT: F 539 ASP cc_start: 0.9122 (m-30) cc_final: 0.8669 (m-30) REVERT: G 410 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8304 (pm20) REVERT: G 420 MET cc_start: 0.8880 (tpp) cc_final: 0.8277 (ttp) REVERT: H 191 GLU cc_start: 0.8552 (tp30) cc_final: 0.7754 (tm-30) REVERT: I 77 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7369 (mm) REVERT: I 79 ARG cc_start: 0.8981 (mpp80) cc_final: 0.8689 (mtt-85) REVERT: I 81 MET cc_start: 0.8873 (mmm) cc_final: 0.8540 (mmm) REVERT: I 171 ASN cc_start: 0.9131 (t0) cc_final: 0.8728 (m-40) REVERT: I 316 ASP cc_start: 0.8657 (m-30) cc_final: 0.8230 (p0) REVERT: I 342 ASP cc_start: 0.7102 (t0) cc_final: 0.6800 (t0) outliers start: 52 outliers final: 27 residues processed: 256 average time/residue: 0.1676 time to fit residues: 69.3959 Evaluate side-chains 238 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 418 MET Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 330 HIS Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 418 MET Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 418 MET Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 372 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 167 optimal weight: 10.0000 chunk 303 optimal weight: 0.0370 chunk 43 optimal weight: 20.0000 chunk 343 optimal weight: 0.0470 chunk 131 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 193 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 overall best weight: 3.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 GLN ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.066969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.048231 restraints weight = 118613.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.049521 restraints weight = 51251.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.050330 restraints weight = 29255.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.050869 restraints weight = 19950.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.051216 restraints weight = 15349.982| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27307 Z= 0.162 Angle : 0.535 9.950 37015 Z= 0.285 Chirality : 0.043 0.259 4195 Planarity : 0.004 0.044 4819 Dihedral : 4.140 21.806 3723 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.94 % Allowed : 13.07 % Favored : 84.99 % 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: 0.19 (0.14), residues: 3432 helix: 2.01 (0.18), residues: 868 sheet: 0.34 (0.16), residues: 954 loop : -1.09 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 156 TYR 0.012 0.001 TYR C 196 PHE 0.019 0.001 PHE I 84 TRP 0.007 0.001 TRP B 372 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00359 (27307) covalent geometry : angle 0.53517 (37015) hydrogen bonds : bond 0.05650 ( 1101) hydrogen bonds : angle 4.75952 ( 3162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 134 MET cc_start: 0.7054 (pmm) cc_final: 0.6800 (pmm) REVERT: A 140 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9204 (mm) REVERT: A 220 MET cc_start: 0.9177 (tpp) cc_final: 0.8944 (tpp) REVERT: B 518 LEU cc_start: 0.9375 (mt) cc_final: 0.8767 (pp) REVERT: C 134 MET cc_start: 0.8412 (mpp) cc_final: 0.8009 (pmm) REVERT: C 362 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: D 418 MET cc_start: 0.9142 (tpp) cc_final: 0.7937 (mmm) REVERT: E 478 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8816 (mp) REVERT: F 195 VAL cc_start: 0.9613 (m) cc_final: 0.9371 (p) REVERT: F 220 MET cc_start: 0.9300 (mmm) cc_final: 0.9079 (mmm) REVERT: F 356 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8582 (mp0) REVERT: F 420 MET cc_start: 0.8713 (tpp) cc_final: 0.8255 (tpt) REVERT: G 410 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8370 (pm20) REVERT: G 420 MET cc_start: 0.8918 (tpp) cc_final: 0.8360 (ttp) REVERT: H 191 GLU cc_start: 0.8618 (tp30) cc_final: 0.7836 (tm-30) REVERT: I 77 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7564 (mm) REVERT: I 79 ARG cc_start: 0.8974 (mpp80) cc_final: 0.8480 (mmt90) REVERT: I 316 ASP cc_start: 0.8799 (m-30) cc_final: 0.8399 (p0) REVERT: I 342 ASP cc_start: 0.7179 (t0) cc_final: 0.6807 (t0) outliers start: 56 outliers final: 37 residues processed: 245 average time/residue: 0.1625 time to fit residues: 64.4073 Evaluate side-chains 243 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 548 MET Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 269 CYS Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain E residue 418 MET Chi-restraints excluded: chain E residue 478 ILE Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 269 CYS Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 330 HIS Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 418 MET Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 418 MET Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 233 ASP Chi-restraints excluded: chain I residue 372 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 189 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 chunk 290 optimal weight: 0.0050 chunk 270 optimal weight: 0.3980 chunk 160 optimal weight: 4.9990 chunk 324 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 overall best weight: 4.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.066519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.047724 restraints weight = 119087.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.049008 restraints weight = 51487.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.049825 restraints weight = 29435.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.050348 restraints weight = 20012.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050680 restraints weight = 15475.443| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 27307 Z= 0.183 Angle : 0.555 10.406 37015 Z= 0.296 Chirality : 0.044 0.218 4195 Planarity : 0.004 0.043 4819 Dihedral : 4.254 21.603 3723 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.05 % Allowed : 13.52 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3432 helix: 2.01 (0.18), residues: 854 sheet: 0.23 (0.16), residues: 965 loop : -1.08 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 156 TYR 0.013 0.001 TYR C 196 PHE 0.023 0.001 PHE I 84 TRP 0.010 0.001 TRP B 372 HIS 0.003 0.001 HIS I 314 Details of bonding type rmsd covalent geometry : bond 0.00408 (27307) covalent geometry : angle 0.55534 (37015) hydrogen bonds : bond 0.05857 ( 1101) hydrogen bonds : angle 4.81400 ( 3162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 207 time to evaluate : 1.066 Fit side-chains REVERT: A 134 MET cc_start: 0.7120 (pmm) cc_final: 0.6838 (pmm) REVERT: A 140 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9219 (mm) REVERT: A 220 MET cc_start: 0.9189 (tpp) cc_final: 0.8947 (tpp) REVERT: B 518 LEU cc_start: 0.9380 (mt) cc_final: 0.8772 (pp) REVERT: C 134 MET cc_start: 0.8197 (mpp) cc_final: 0.7851 (pmm) REVERT: C 362 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: C 390 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8832 (m-80) REVERT: D 341 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: D 418 MET cc_start: 0.9169 (tpp) cc_final: 0.7918 (mmm) REVERT: E 478 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8910 (mp) REVERT: F 195 VAL cc_start: 0.9618 (OUTLIER) cc_final: 0.9388 (p) REVERT: F 220 MET cc_start: 0.9295 (mmm) cc_final: 0.9088 (mmm) REVERT: F 356 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8609 (mp0) REVERT: G 410 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8386 (pm20) REVERT: G 420 MET cc_start: 0.8903 (tpp) cc_final: 0.8378 (ttp) REVERT: H 191 GLU cc_start: 0.8607 (tp30) cc_final: 0.7888 (tm-30) REVERT: I 77 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7336 (mm) REVERT: I 79 ARG cc_start: 0.8972 (mpp80) cc_final: 0.8450 (mmt90) REVERT: I 316 ASP cc_start: 0.8897 (m-30) cc_final: 0.8452 (p0) REVERT: I 342 ASP cc_start: 0.7232 (t0) cc_final: 0.6767 (t0) outliers start: 59 outliers final: 40 residues processed: 246 average time/residue: 0.1683 time to fit residues: 67.1686 Evaluate side-chains 245 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 548 MET Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 269 CYS Chi-restraints excluded: chain E residue 418 MET Chi-restraints excluded: chain E residue 478 ILE Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 269 CYS Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 330 HIS Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 418 MET Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 418 MET Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 233 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 144 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 264 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 GLN G 360 HIS H 145 GLN ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.067275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.048545 restraints weight = 117704.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.049843 restraints weight = 51003.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.050669 restraints weight = 29180.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.051195 restraints weight = 19874.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.051538 restraints weight = 15312.717| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27307 Z= 0.149 Angle : 0.542 9.986 37015 Z= 0.288 Chirality : 0.043 0.204 4195 Planarity : 0.003 0.044 4819 Dihedral : 4.163 21.602 3723 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.12 % Allowed : 13.94 % Favored : 83.95 % 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 (0.14), residues: 3432 helix: 1.98 (0.18), residues: 862 sheet: 0.26 (0.17), residues: 965 loop : -1.08 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 156 TYR 0.012 0.001 TYR E 196 PHE 0.025 0.001 PHE I 84 TRP 0.008 0.001 TRP B 372 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00328 (27307) covalent geometry : angle 0.54211 (37015) hydrogen bonds : bond 0.05611 ( 1101) hydrogen bonds : angle 4.68666 ( 3162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 205 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.7041 (pmm) cc_final: 0.6753 (pmm) REVERT: A 140 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9225 (mm) REVERT: A 220 MET cc_start: 0.9276 (tpp) cc_final: 0.9011 (tpp) REVERT: B 518 LEU cc_start: 0.9375 (mt) cc_final: 0.8763 (pp) REVERT: C 134 MET cc_start: 0.8203 (mpp) cc_final: 0.7844 (pmm) REVERT: C 362 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: C 390 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8731 (m-80) REVERT: D 418 MET cc_start: 0.9176 (tpp) cc_final: 0.8856 (mmm) REVERT: E 478 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8836 (mp) REVERT: F 195 VAL cc_start: 0.9616 (OUTLIER) cc_final: 0.9388 (p) REVERT: F 220 MET cc_start: 0.9292 (mmm) cc_final: 0.9064 (mmm) REVERT: F 356 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8580 (mp0) REVERT: G 410 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: G 420 MET cc_start: 0.8832 (tpp) cc_final: 0.8395 (ttp) REVERT: H 191 GLU cc_start: 0.8611 (tp30) cc_final: 0.7885 (tm-30) REVERT: I 77 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7280 (mm) REVERT: I 79 ARG cc_start: 0.8962 (mpp80) cc_final: 0.8465 (mmt90) REVERT: I 342 ASP cc_start: 0.7290 (t0) cc_final: 0.6834 (t0) outliers start: 61 outliers final: 39 residues processed: 246 average time/residue: 0.1624 time to fit residues: 64.6212 Evaluate side-chains 247 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 548 MET Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 269 CYS Chi-restraints excluded: chain E residue 418 MET Chi-restraints excluded: chain E residue 478 ILE Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 269 CYS Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 330 HIS Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 418 MET Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 418 MET Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 233 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 226 optimal weight: 20.0000 chunk 228 optimal weight: 30.0000 chunk 177 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 19 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 GLN ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.067396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.048630 restraints weight = 117901.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.049919 restraints weight = 51056.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.050750 restraints weight = 29332.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.051237 restraints weight = 19934.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.051603 restraints weight = 15527.962| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27307 Z= 0.154 Angle : 0.550 10.464 37015 Z= 0.292 Chirality : 0.043 0.185 4195 Planarity : 0.004 0.043 4819 Dihedral : 4.164 21.511 3723 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.01 % Allowed : 13.94 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3432 helix: 2.00 (0.18), residues: 861 sheet: 0.24 (0.17), residues: 961 loop : -1.07 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 156 TYR 0.012 0.001 TYR C 196 PHE 0.028 0.001 PHE I 84 TRP 0.009 0.001 TRP B 372 HIS 0.002 0.001 HIS I 314 Details of bonding type rmsd covalent geometry : bond 0.00341 (27307) covalent geometry : angle 0.55032 (37015) hydrogen bonds : bond 0.05610 ( 1101) hydrogen bonds : angle 4.68371 ( 3162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 202 time to evaluate : 1.122 Fit side-chains REVERT: A 134 MET cc_start: 0.7053 (pmm) cc_final: 0.6757 (pmm) REVERT: A 140 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9229 (mm) REVERT: A 220 MET cc_start: 0.9306 (tpp) cc_final: 0.9075 (tpp) REVERT: C 134 MET cc_start: 0.8203 (mpp) cc_final: 0.7844 (pmm) REVERT: C 362 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8246 (tm-30) REVERT: C 390 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8774 (m-80) REVERT: D 364 MET cc_start: 0.9141 (mmm) cc_final: 0.8759 (mpp) REVERT: D 418 MET cc_start: 0.9177 (tpp) cc_final: 0.8854 (mmm) REVERT: E 478 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8845 (mp) REVERT: F 195 VAL cc_start: 0.9618 (OUTLIER) cc_final: 0.9393 (p) REVERT: F 220 MET cc_start: 0.9289 (mmm) cc_final: 0.9048 (mmm) REVERT: F 356 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8576 (mp0) REVERT: F 420 MET cc_start: 0.8783 (tpp) cc_final: 0.8429 (tpp) REVERT: G 410 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: G 420 MET cc_start: 0.8831 (tpp) cc_final: 0.8383 (ttp) REVERT: H 145 GLN cc_start: 0.8446 (pp30) cc_final: 0.8169 (pp30) REVERT: H 191 GLU cc_start: 0.8611 (tp30) cc_final: 0.7876 (tm-30) REVERT: I 77 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7212 (mm) REVERT: I 316 ASP cc_start: 0.8838 (m-30) cc_final: 0.8444 (p0) REVERT: I 342 ASP cc_start: 0.7287 (t0) cc_final: 0.6838 (t0) outliers start: 58 outliers final: 42 residues processed: 241 average time/residue: 0.1594 time to fit residues: 62.7430 Evaluate side-chains 248 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 548 MET Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 269 CYS Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain E residue 418 MET Chi-restraints excluded: chain E residue 478 ILE Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 269 CYS Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 330 HIS Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 418 MET Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 233 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 133 optimal weight: 8.9990 chunk 189 optimal weight: 20.0000 chunk 249 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 306 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 chunk 254 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 301 optimal weight: 9.9990 chunk 325 optimal weight: 1.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.065804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.047057 restraints weight = 118570.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.048306 restraints weight = 51587.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.049086 restraints weight = 29682.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.049615 restraints weight = 20354.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.049902 restraints weight = 15754.698| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 27307 Z= 0.272 Angle : 0.640 11.531 37015 Z= 0.341 Chirality : 0.045 0.196 4195 Planarity : 0.004 0.041 4819 Dihedral : 4.628 20.404 3723 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.01 % Allowed : 14.15 % Favored : 83.84 % 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: -0.05 (0.14), residues: 3432 helix: 1.81 (0.18), residues: 855 sheet: 0.19 (0.17), residues: 931 loop : -1.19 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 368 TYR 0.017 0.002 TYR F 357 PHE 0.022 0.001 PHE I 84 TRP 0.014 0.002 TRP B 372 HIS 0.004 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00615 (27307) covalent geometry : angle 0.63979 (37015) hydrogen bonds : bond 0.06514 ( 1101) hydrogen bonds : angle 5.06766 ( 3162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 140 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9226 (mm) REVERT: A 220 MET cc_start: 0.9328 (tpp) cc_final: 0.8936 (tpp) REVERT: C 134 MET cc_start: 0.8208 (mpp) cc_final: 0.7855 (pmm) REVERT: C 362 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8288 (tm-30) REVERT: C 390 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8860 (m-80) REVERT: D 418 MET cc_start: 0.9247 (tpp) cc_final: 0.8943 (mmm) REVERT: E 370 MET cc_start: 0.8926 (mtm) cc_final: 0.8350 (mtt) REVERT: E 478 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8963 (mp) REVERT: F 220 MET cc_start: 0.9316 (mmm) cc_final: 0.9095 (mmm) REVERT: F 356 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8686 (mp0) REVERT: F 420 MET cc_start: 0.8835 (tpp) cc_final: 0.8416 (tpp) REVERT: G 356 GLU cc_start: 0.8258 (tt0) cc_final: 0.8052 (tm-30) REVERT: G 410 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8376 (pm20) REVERT: G 420 MET cc_start: 0.8853 (tpp) cc_final: 0.8497 (ttp) REVERT: H 145 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8264 (pp30) REVERT: H 163 PHE cc_start: 0.8613 (t80) cc_final: 0.8147 (t80) REVERT: H 191 GLU cc_start: 0.8660 (tp30) cc_final: 0.8027 (tm-30) REVERT: I 77 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7261 (mm) REVERT: I 316 ASP cc_start: 0.8796 (m-30) cc_final: 0.8502 (p0) REVERT: I 342 ASP cc_start: 0.7362 (t0) cc_final: 0.6915 (t0) outliers start: 58 outliers final: 41 residues processed: 244 average time/residue: 0.1611 time to fit residues: 62.8524 Evaluate side-chains 248 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 548 MET Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 269 CYS Chi-restraints excluded: chain E residue 418 MET Chi-restraints excluded: chain E residue 478 ILE Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 269 CYS Chi-restraints excluded: chain F residue 330 HIS Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 418 MET Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 418 MET Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 233 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 291 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 chunk 268 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 311 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 84 optimal weight: 30.0000 chunk 160 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 GLN ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.048134 restraints weight = 118825.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.049418 restraints weight = 51339.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.050229 restraints weight = 29434.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.050709 restraints weight = 20092.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.051072 restraints weight = 15725.282| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27307 Z= 0.164 Angle : 0.576 10.867 37015 Z= 0.305 Chirality : 0.044 0.181 4195 Planarity : 0.004 0.042 4819 Dihedral : 4.356 21.189 3723 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.63 % Allowed : 14.56 % Favored : 83.81 % 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: 0.03 (0.14), residues: 3432 helix: 1.94 (0.18), residues: 855 sheet: 0.20 (0.17), residues: 944 loop : -1.15 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 156 TYR 0.013 0.001 TYR C 405 PHE 0.034 0.001 PHE I 84 TRP 0.010 0.001 TRP B 372 HIS 0.002 0.001 HIS G 360 Details of bonding type rmsd covalent geometry : bond 0.00363 (27307) covalent geometry : angle 0.57621 (37015) hydrogen bonds : bond 0.05864 ( 1101) hydrogen bonds : angle 4.81041 ( 3162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 1.046 Fit side-chains REVERT: A 140 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9157 (mm) REVERT: A 220 MET cc_start: 0.9317 (tpp) cc_final: 0.8917 (tpp) REVERT: C 134 MET cc_start: 0.8201 (mpp) cc_final: 0.7845 (pmm) REVERT: C 362 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: C 390 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8767 (m-80) REVERT: D 418 MET cc_start: 0.9223 (tpp) cc_final: 0.8916 (mmm) REVERT: E 370 MET cc_start: 0.8957 (mtm) cc_final: 0.8743 (mtt) REVERT: E 478 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8928 (mp) REVERT: F 220 MET cc_start: 0.9301 (mmm) cc_final: 0.9068 (mmm) REVERT: F 356 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8587 (mp0) REVERT: F 420 MET cc_start: 0.8783 (tpp) cc_final: 0.8278 (tpt) REVERT: G 410 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8397 (pm20) REVERT: G 420 MET cc_start: 0.8850 (tpp) cc_final: 0.8444 (ttt) REVERT: H 145 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8212 (pp30) REVERT: H 163 PHE cc_start: 0.8536 (t80) cc_final: 0.8307 (t80) REVERT: H 191 GLU cc_start: 0.8631 (tp30) cc_final: 0.7971 (tm-30) REVERT: I 77 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7188 (mm) REVERT: I 316 ASP cc_start: 0.8829 (m-30) cc_final: 0.8579 (p0) REVERT: I 342 ASP cc_start: 0.7238 (t0) cc_final: 0.6806 (t0) outliers start: 47 outliers final: 38 residues processed: 235 average time/residue: 0.1659 time to fit residues: 63.0185 Evaluate side-chains 244 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 548 MET Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 269 CYS Chi-restraints excluded: chain E residue 478 ILE Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 269 CYS Chi-restraints excluded: chain F residue 330 HIS Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 418 MET Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 233 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 61 optimal weight: 10.0000 chunk 257 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 329 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 GLN ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.047460 restraints weight = 118202.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.048722 restraints weight = 51301.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.049533 restraints weight = 29385.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.050047 restraints weight = 20006.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.050359 restraints weight = 15450.609| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 27307 Z= 0.203 Angle : 0.597 10.930 37015 Z= 0.317 Chirality : 0.044 0.191 4195 Planarity : 0.004 0.042 4819 Dihedral : 4.439 20.714 3723 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.73 % Allowed : 14.60 % Favored : 83.67 % 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: -0.01 (0.14), residues: 3432 helix: 1.86 (0.18), residues: 858 sheet: 0.17 (0.17), residues: 936 loop : -1.13 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 368 TYR 0.014 0.002 TYR G 452 PHE 0.032 0.001 PHE I 84 TRP 0.012 0.001 TRP B 372 HIS 0.003 0.001 HIS G 360 Details of bonding type rmsd covalent geometry : bond 0.00457 (27307) covalent geometry : angle 0.59743 (37015) hydrogen bonds : bond 0.06068 ( 1101) hydrogen bonds : angle 4.89047 ( 3162) =============================================================================== Job complete usr+sys time: 5464.66 seconds wall clock time: 94 minutes 52.86 seconds (5692.86 seconds total)