Starting phenix.real_space_refine on Sat Mar 7 01:48:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xx2_33498/03_2026/7xx2_33498.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xx2_33498/03_2026/7xx2_33498.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xx2_33498/03_2026/7xx2_33498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xx2_33498/03_2026/7xx2_33498.map" model { file = "/net/cci-nas-00/data/ceres_data/7xx2_33498/03_2026/7xx2_33498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xx2_33498/03_2026/7xx2_33498.cif" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 194 5.16 5 C 23337 2.51 5 N 6133 2.21 5 O 6757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36436 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6617 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 32, 'TRANS': 794} Chain breaks: 2 Chain: "B" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3196 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 380} Chain breaks: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 6617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6617 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 32, 'TRANS': 794} Chain breaks: 2 Chain: "E" Number of atoms: 6617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6617 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 32, 'TRANS': 794} Chain breaks: 2 Chain: "G" Number of atoms: 6617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6617 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 32, 'TRANS': 794} Chain breaks: 2 Chain: "I" Number of atoms: 6617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6617 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 32, 'TRANS': 794} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.02, per 1000 atoms: 0.22 Number of scatterers: 36436 At special positions: 0 Unit cell: (184.21, 168.95, 183.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 194 16.00 P 15 15.00 O 6757 8.00 N 6133 7.00 C 23337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.5 seconds 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8582 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 34 sheets defined 42.5% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 24 through 52 removed outlier: 4.147A pdb=" N LYS A 28 " --> pdb=" O THR A 24 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 87 Processing helix chain 'A' and resid 116 through 141 removed outlier: 3.725A pdb=" N GLU A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 170 through 181 removed outlier: 4.203A pdb=" N THR A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 Processing helix chain 'A' and resid 234 through 247 removed outlier: 3.572A pdb=" N ASP A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.999A pdb=" N ILE A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N CYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.858A pdb=" N SER A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 317' Processing helix chain 'A' and resid 333 through 345 Processing helix chain 'A' and resid 356 through 368 Processing helix chain 'A' and resid 370 through 382 Processing helix chain 'A' and resid 391 through 400 Processing helix chain 'A' and resid 410 through 424 removed outlier: 3.738A pdb=" N LYS A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 416 " --> pdb=" O GLN A 412 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SER A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 434 Processing helix chain 'A' and resid 435 through 438 Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 469 through 482 Processing helix chain 'A' and resid 502 through 516 removed outlier: 4.175A pdb=" N GLU A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 615 through 621 removed outlier: 3.740A pdb=" N ILE A 618 " --> pdb=" O PRO A 615 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY A 619 " --> pdb=" O MET A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 665 Processing helix chain 'A' and resid 680 through 687 removed outlier: 3.668A pdb=" N LEU A 687 " --> pdb=" O PHE A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 716 removed outlier: 3.903A pdb=" N LYS A 709 " --> pdb=" O GLN A 705 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 793 removed outlier: 3.938A pdb=" N ILE A 788 " --> pdb=" O ARG A 784 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Processing helix chain 'A' and resid 862 through 864 No H-bonds generated for 'chain 'A' and resid 862 through 864' Processing helix chain 'B' and resid 141 through 150 removed outlier: 4.189A pdb=" N ILE B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 193 removed outlier: 3.959A pdb=" N ASN B 189 " --> pdb=" O PHE B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 226 removed outlier: 3.572A pdb=" N LEU B 214 " --> pdb=" O TRP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 242 removed outlier: 4.708A pdb=" N GLU B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 removed outlier: 3.527A pdb=" N SER B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.701A pdb=" N THR B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 317 removed outlier: 3.856A pdb=" N LEU B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASP B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.667A pdb=" N ILE B 322 " --> pdb=" O ASN B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 347 removed outlier: 4.144A pdb=" N PHE B 339 " --> pdb=" O HIS B 335 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B 343 " --> pdb=" O PHE B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 365 removed outlier: 3.761A pdb=" N SER B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 391 removed outlier: 3.814A pdb=" N TYR B 383 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 Processing helix chain 'B' and resid 423 through 441 removed outlier: 3.730A pdb=" N ARG B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 455 removed outlier: 3.685A pdb=" N LYS B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 483 removed outlier: 3.669A pdb=" N GLU B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 482 " --> pdb=" O ARG B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 527 Processing helix chain 'B' and resid 533 through 538 removed outlier: 3.578A pdb=" N GLN B 538 " --> pdb=" O ASN B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 552 Processing helix chain 'C' and resid 25 through 51 removed outlier: 4.032A pdb=" N VAL C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 87 Processing helix chain 'C' and resid 116 through 140 Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 164 through 168 removed outlier: 3.697A pdb=" N GLU C 167 " --> pdb=" O ASP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 183 removed outlier: 4.242A pdb=" N THR C 174 " --> pdb=" O GLY C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 217 removed outlier: 3.502A pdb=" N LYS C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 247 removed outlier: 3.547A pdb=" N ASP C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.749A pdb=" N ILE C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 322 through 326 Processing helix chain 'C' and resid 333 through 346 removed outlier: 3.501A pdb=" N ILE C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 368 removed outlier: 3.506A pdb=" N LYS C 366 " --> pdb=" O GLU C 362 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS C 367 " --> pdb=" O ILE C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 382 Processing helix chain 'C' and resid 391 through 400 removed outlier: 3.501A pdb=" N ILE C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 424 removed outlier: 4.485A pdb=" N ILE C 416 " --> pdb=" O GLN C 412 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 434 Processing helix chain 'C' and resid 435 through 438 Processing helix chain 'C' and resid 446 through 457 Processing helix chain 'C' and resid 469 through 482 Processing helix chain 'C' and resid 502 through 516 removed outlier: 3.914A pdb=" N GLU C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 597 removed outlier: 4.315A pdb=" N GLY C 596 " --> pdb=" O GLY C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 621 removed outlier: 3.586A pdb=" N ILE C 618 " --> pdb=" O PRO C 615 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY C 619 " --> pdb=" O MET C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 665 Processing helix chain 'C' and resid 680 through 687 removed outlier: 3.938A pdb=" N LEU C 687 " --> pdb=" O PHE C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 715 removed outlier: 3.835A pdb=" N LYS C 709 " --> pdb=" O GLN C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 718 No H-bonds generated for 'chain 'C' and resid 716 through 718' Processing helix chain 'C' and resid 784 through 793 removed outlier: 4.105A pdb=" N ILE C 788 " --> pdb=" O ARG C 784 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN C 789 " --> pdb=" O SER C 785 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR C 793 " --> pdb=" O GLN C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 810 Processing helix chain 'C' and resid 862 through 864 No H-bonds generated for 'chain 'C' and resid 862 through 864' Processing helix chain 'E' and resid 25 through 52 removed outlier: 3.870A pdb=" N VAL E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU E 34 " --> pdb=" O ARG E 30 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 87 Processing helix chain 'E' and resid 116 through 141 removed outlier: 3.592A pdb=" N GLU E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 163 removed outlier: 3.528A pdb=" N THR E 163 " --> pdb=" O ALA E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 168 removed outlier: 3.670A pdb=" N LEU E 168 " --> pdb=" O VAL E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 184 removed outlier: 3.609A pdb=" N THR E 174 " --> pdb=" O GLY E 170 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 182 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU E 184 " --> pdb=" O ASN E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 217 Processing helix chain 'E' and resid 234 through 247 removed outlier: 3.529A pdb=" N ASP E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 272 Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.771A pdb=" N ILE E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 317 removed outlier: 3.607A pdb=" N SER E 316 " --> pdb=" O ASN E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 346 Processing helix chain 'E' and resid 356 through 368 removed outlier: 3.638A pdb=" N LYS E 366 " --> pdb=" O GLU E 362 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS E 367 " --> pdb=" O ILE E 363 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY E 368 " --> pdb=" O LEU E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 382 removed outlier: 3.998A pdb=" N ALA E 378 " --> pdb=" O ILE E 374 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 382 " --> pdb=" O ALA E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 400 Processing helix chain 'E' and resid 410 through 424 removed outlier: 4.285A pdb=" N ILE E 416 " --> pdb=" O GLN E 412 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER E 420 " --> pdb=" O ILE E 416 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR E 421 " --> pdb=" O LEU E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 434 Processing helix chain 'E' and resid 435 through 438 removed outlier: 3.517A pdb=" N PHE E 438 " --> pdb=" O LEU E 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 435 through 438' Processing helix chain 'E' and resid 446 through 457 Processing helix chain 'E' and resid 468 through 482 removed outlier: 3.669A pdb=" N GLY E 472 " --> pdb=" O LEU E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 515 Processing helix chain 'E' and resid 615 through 621 removed outlier: 3.760A pdb=" N ILE E 618 " --> pdb=" O PRO E 615 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY E 619 " --> pdb=" O MET E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 687 removed outlier: 3.763A pdb=" N LEU E 687 " --> pdb=" O PHE E 683 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 690 No H-bonds generated for 'chain 'E' and resid 688 through 690' Processing helix chain 'E' and resid 705 through 716 removed outlier: 3.775A pdb=" N LYS E 709 " --> pdb=" O GLN E 705 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER E 716 " --> pdb=" O GLU E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 784 through 793 removed outlier: 4.093A pdb=" N ILE E 788 " --> pdb=" O ARG E 784 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN E 789 " --> pdb=" O SER E 785 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR E 793 " --> pdb=" O GLN E 789 " (cutoff:3.500A) Processing helix chain 'E' and resid 805 through 810 Processing helix chain 'E' and resid 840 through 844 removed outlier: 4.452A pdb=" N PHE E 844 " --> pdb=" O PRO E 841 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 864 No H-bonds generated for 'chain 'E' and resid 862 through 864' Processing helix chain 'G' and resid 25 through 53 removed outlier: 3.522A pdb=" N SER G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL G 53 " --> pdb=" O LYS G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 87 Processing helix chain 'G' and resid 116 through 140 Processing helix chain 'G' and resid 155 through 162 removed outlier: 3.996A pdb=" N MET G 159 " --> pdb=" O PRO G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 168 removed outlier: 3.598A pdb=" N GLU G 167 " --> pdb=" O ASP G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 184 removed outlier: 3.616A pdb=" N LEU G 182 " --> pdb=" O LEU G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 217 removed outlier: 3.532A pdb=" N LYS G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 247 removed outlier: 3.656A pdb=" N ASP G 247 " --> pdb=" O LEU G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 272 removed outlier: 3.827A pdb=" N LEU G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 295 removed outlier: 3.607A pdb=" N ILE G 293 " --> pdb=" O ALA G 289 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 318 Processing helix chain 'G' and resid 333 through 346 removed outlier: 3.558A pdb=" N ILE G 345 " --> pdb=" O PHE G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 368 removed outlier: 3.595A pdb=" N LYS G 366 " --> pdb=" O GLU G 362 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS G 367 " --> pdb=" O ILE G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 382 Processing helix chain 'G' and resid 391 through 400 Processing helix chain 'G' and resid 410 through 424 removed outlier: 3.520A pdb=" N LYS G 414 " --> pdb=" O LEU G 410 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE G 416 " --> pdb=" O GLN G 412 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 417 " --> pdb=" O MET G 413 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER G 420 " --> pdb=" O ILE G 416 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR G 421 " --> pdb=" O LEU G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 428 through 434 Processing helix chain 'G' and resid 435 through 438 Processing helix chain 'G' and resid 446 through 457 Processing helix chain 'G' and resid 469 through 482 Processing helix chain 'G' and resid 502 through 515 Processing helix chain 'G' and resid 615 through 621 removed outlier: 3.594A pdb=" N ILE G 618 " --> pdb=" O PRO G 615 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY G 619 " --> pdb=" O MET G 616 " (cutoff:3.500A) Processing helix chain 'G' and resid 661 through 665 removed outlier: 4.136A pdb=" N ASN G 664 " --> pdb=" O GLY G 661 " (cutoff:3.500A) Processing helix chain 'G' and resid 680 through 688 removed outlier: 3.515A pdb=" N VAL G 684 " --> pdb=" O ASP G 680 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 687 " --> pdb=" O PHE G 683 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY G 688 " --> pdb=" O VAL G 684 " (cutoff:3.500A) Processing helix chain 'G' and resid 705 through 717 removed outlier: 3.900A pdb=" N LYS G 709 " --> pdb=" O GLN G 705 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER G 716 " --> pdb=" O GLU G 712 " (cutoff:3.500A) Processing helix chain 'G' and resid 786 through 793 Processing helix chain 'G' and resid 805 through 810 Processing helix chain 'G' and resid 862 through 864 No H-bonds generated for 'chain 'G' and resid 862 through 864' Processing helix chain 'I' and resid 25 through 52 removed outlier: 3.820A pdb=" N VAL I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU I 34 " --> pdb=" O ARG I 30 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER I 35 " --> pdb=" O LYS I 31 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS I 52 " --> pdb=" O SER I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 87 Processing helix chain 'I' and resid 116 through 141 removed outlier: 3.822A pdb=" N GLU I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU I 137 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG I 138 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN I 139 " --> pdb=" O ALA I 135 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR I 141 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 163 removed outlier: 3.727A pdb=" N MET I 159 " --> pdb=" O PRO I 156 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA I 160 " --> pdb=" O ARG I 157 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU I 161 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR I 162 " --> pdb=" O MET I 159 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR I 163 " --> pdb=" O ALA I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 184 removed outlier: 3.511A pdb=" N MET I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 217 Processing helix chain 'I' and resid 234 through 247 Processing helix chain 'I' and resid 260 through 272 removed outlier: 4.316A pdb=" N LEU I 264 " --> pdb=" O ASP I 260 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE I 265 " --> pdb=" O GLU I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 294 removed outlier: 3.578A pdb=" N ILE I 293 " --> pdb=" O ALA I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 297 No H-bonds generated for 'chain 'I' and resid 295 through 297' Processing helix chain 'I' and resid 313 through 318 removed outlier: 3.558A pdb=" N ALA I 318 " --> pdb=" O SER I 314 " (cutoff:3.500A) Processing helix chain 'I' and resid 333 through 345 Processing helix chain 'I' and resid 356 through 368 removed outlier: 3.813A pdb=" N LYS I 366 " --> pdb=" O GLU I 362 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS I 367 " --> pdb=" O ILE I 363 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY I 368 " --> pdb=" O LEU I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 370 through 382 removed outlier: 3.593A pdb=" N ILE I 374 " --> pdb=" O VAL I 370 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA I 382 " --> pdb=" O ALA I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 391 through 400 Processing helix chain 'I' and resid 410 through 424 removed outlier: 3.555A pdb=" N LYS I 414 " --> pdb=" O LEU I 410 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS I 415 " --> pdb=" O GLU I 411 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE I 416 " --> pdb=" O GLN I 412 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER I 420 " --> pdb=" O ILE I 416 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR I 421 " --> pdb=" O LEU I 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 434 Processing helix chain 'I' and resid 435 through 438 Processing helix chain 'I' and resid 446 through 457 Processing helix chain 'I' and resid 469 through 482 Processing helix chain 'I' and resid 502 through 516 removed outlier: 4.496A pdb=" N GLU I 516 " --> pdb=" O LEU I 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 616 through 621 removed outlier: 4.464A pdb=" N GLY I 619 " --> pdb=" O MET I 616 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS I 620 " --> pdb=" O GLU I 617 " (cutoff:3.500A) Processing helix chain 'I' and resid 661 through 665 Processing helix chain 'I' and resid 680 through 688 removed outlier: 3.576A pdb=" N LEU I 687 " --> pdb=" O PHE I 683 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY I 688 " --> pdb=" O VAL I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 718 removed outlier: 4.024A pdb=" N LYS I 709 " --> pdb=" O GLN I 705 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET I 718 " --> pdb=" O SER I 714 " (cutoff:3.500A) Processing helix chain 'I' and resid 784 through 792 removed outlier: 3.781A pdb=" N ILE I 788 " --> pdb=" O ARG I 784 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN I 789 " --> pdb=" O SER I 785 " (cutoff:3.500A) Processing helix chain 'I' and resid 805 through 810 Processing helix chain 'I' and resid 862 through 864 No H-bonds generated for 'chain 'I' and resid 862 through 864' Processing sheet with id=AA1, first strand: chain 'A' and resid 226 through 228 removed outlier: 6.829A pdb=" N VAL A 227 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N TYR A 327 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER A 197 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 444 through 445 removed outlier: 6.687A pdb=" N VAL A 496 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE A 490 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 498 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.870A pdb=" N THR A 520 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 539 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 559 " --> pdb=" O ASP A 583 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU A 604 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 649 through 651 removed outlier: 6.882A pdb=" N LEU A 650 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU A 674 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 695 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASP A 672 " --> pdb=" O VAL A 695 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG A 697 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 696 " --> pdb=" O SER A 723 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A 725 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 700 " --> pdb=" O PHE A 727 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 778 through 780 removed outlier: 3.509A pdb=" N CYS A 832 " --> pdb=" O ARG A 854 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 858 through 860 Processing sheet with id=AA7, first strand: chain 'C' and resid 225 through 228 removed outlier: 6.033A pdb=" N ALA C 225 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASP C 282 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL C 227 " --> pdb=" O ASP C 282 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS C 194 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR C 308 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE C 196 " --> pdb=" O THR C 308 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR C 310 " --> pdb=" O ILE C 196 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE C 198 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR C 327 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER C 197 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 444 through 445 removed outlier: 6.970A pdb=" N VAL C 496 " --> pdb=" O ILE C 490 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE C 490 " --> pdb=" O VAL C 496 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.905A pdb=" N THR C 520 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL C 559 " --> pdb=" O ASP C 583 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 626 through 628 removed outlier: 6.804A pdb=" N LEU C 627 " --> pdb=" O TYR C 651 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU C 650 " --> pdb=" O ASP C 672 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU C 674 " --> pdb=" O LEU C 650 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL C 695 " --> pdb=" O VAL C 670 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASP C 672 " --> pdb=" O VAL C 695 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG C 697 " --> pdb=" O ASP C 672 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 699 " --> pdb=" O LEU C 674 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 778 through 780 removed outlier: 6.467A pdb=" N LEU C 800 " --> pdb=" O ARG C 833 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE C 835 " --> pdb=" O LEU C 800 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE C 802 " --> pdb=" O ILE C 835 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS C 832 " --> pdb=" O ARG C 854 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP C 856 " --> pdb=" O CYS C 832 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 858 through 860 removed outlier: 6.805A pdb=" N PHE C 859 " --> pdb=" O ILE C 887 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 225 through 228 removed outlier: 6.129A pdb=" N ALA E 225 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASP E 282 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL E 227 " --> pdb=" O ASP E 282 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR E 309 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N TYR E 327 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER E 197 " --> pdb=" O TYR E 327 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 444 through 445 removed outlier: 7.218A pdb=" N GLY E 489 " --> pdb=" O LYS E 497 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N CYS E 499 " --> pdb=" O PRO E 487 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.569A pdb=" N THR E 520 " --> pdb=" O SER E 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 558 through 560 removed outlier: 6.487A pdb=" N VAL E 559 " --> pdb=" O ASP E 583 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 626 through 628 removed outlier: 6.714A pdb=" N LEU E 627 " --> pdb=" O TYR E 651 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU E 650 " --> pdb=" O ASP E 672 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU E 674 " --> pdb=" O LEU E 650 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP E 673 " --> pdb=" O ARG E 697 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASP E 699 " --> pdb=" O ASP E 673 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY E 675 " --> pdb=" O ASP E 699 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU E 696 " --> pdb=" O ASP E 725 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N PHE E 727 " --> pdb=" O LEU E 696 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU E 698 " --> pdb=" O PHE E 727 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 778 through 780 removed outlier: 6.243A pdb=" N LEU E 800 " --> pdb=" O ARG E 833 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE E 835 " --> pdb=" O LEU E 800 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE E 802 " --> pdb=" O ILE E 835 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N CYS E 832 " --> pdb=" O ARG E 854 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 858 through 860 Processing sheet with id=AC2, first strand: chain 'G' and resid 225 through 228 removed outlier: 6.206A pdb=" N ALA G 225 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ASP G 282 " --> pdb=" O ALA G 225 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL G 227 " --> pdb=" O ASP G 282 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE G 279 " --> pdb=" O ARG G 305 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N TYR G 327 " --> pdb=" O THR G 195 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER G 197 " --> pdb=" O TYR G 327 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 444 through 445 removed outlier: 6.712A pdb=" N VAL G 496 " --> pdb=" O ILE G 490 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE G 490 " --> pdb=" O VAL G 496 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 520 through 522 removed outlier: 6.490A pdb=" N THR G 520 " --> pdb=" O SER G 540 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 581 through 583 removed outlier: 6.909A pdb=" N LEU G 582 " --> pdb=" O GLY G 605 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'G' and resid 649 through 651 removed outlier: 3.537A pdb=" N ASP G 672 " --> pdb=" O LEU G 650 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 674 through 676 removed outlier: 3.594A pdb=" N LEU G 696 " --> pdb=" O SER G 723 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP G 725 " --> pdb=" O LEU G 696 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 778 through 780 removed outlier: 6.170A pdb=" N LEU G 800 " --> pdb=" O ARG G 833 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE G 835 " --> pdb=" O LEU G 800 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE G 802 " --> pdb=" O ILE G 835 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 858 through 860 removed outlier: 6.409A pdb=" N PHE G 859 " --> pdb=" O ILE G 887 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'I' and resid 225 through 228 removed outlier: 6.112A pdb=" N ALA I 225 " --> pdb=" O VAL I 280 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASP I 282 " --> pdb=" O ALA I 225 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL I 227 " --> pdb=" O ASP I 282 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N TYR I 327 " --> pdb=" O THR I 195 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER I 197 " --> pdb=" O TYR I 327 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 444 through 445 removed outlier: 6.490A pdb=" N VAL I 496 " --> pdb=" O ILE I 490 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE I 490 " --> pdb=" O VAL I 496 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 519 through 522 removed outlier: 6.408A pdb=" N THR I 520 " --> pdb=" O SER I 540 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU I 539 " --> pdb=" O SER I 558 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR I 560 " --> pdb=" O LEU I 539 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 581 through 583 Processing sheet with id=AD5, first strand: chain 'I' and resid 649 through 651 removed outlier: 3.833A pdb=" N ASP I 672 " --> pdb=" O LEU I 650 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL I 695 " --> pdb=" O VAL I 670 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP I 672 " --> pdb=" O VAL I 695 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARG I 697 " --> pdb=" O ASP I 672 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP I 699 " --> pdb=" O LEU I 674 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N PHE I 727 " --> pdb=" O LEU I 696 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU I 698 " --> pdb=" O PHE I 727 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 778 through 780 removed outlier: 3.555A pdb=" N LEU I 780 " --> pdb=" O TRP I 803 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU I 800 " --> pdb=" O ARG I 833 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE I 835 " --> pdb=" O LEU I 800 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE I 802 " --> pdb=" O ILE I 835 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS I 832 " --> pdb=" O ARG I 854 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP I 856 " --> pdb=" O CYS I 832 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 858 through 860 1262 hydrogen bonds defined for protein. 3597 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: 6.26 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6053 1.32 - 1.44: 9259 1.44 - 1.57: 21497 1.57 - 1.69: 25 1.69 - 1.81: 306 Bond restraints: 37140 Sorted by residual: bond pdb=" C4 ATP G1001 " pdb=" C5 ATP G1001 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.00e+01 bond pdb=" C ALA E 212 " pdb=" O ALA E 212 " ideal model delta sigma weight residual 1.236 1.315 -0.079 1.15e-02 7.56e+03 4.70e+01 bond pdb=" C4 ATP I1001 " pdb=" C5 ATP I1001 " ideal model delta sigma weight residual 1.388 1.451 -0.063 1.00e-02 1.00e+04 4.00e+01 bond pdb=" C4 ATP C1001 " pdb=" C5 ATP C1001 " ideal model delta sigma weight residual 1.388 1.451 -0.063 1.00e-02 1.00e+04 3.94e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.449 -0.061 1.00e-02 1.00e+04 3.71e+01 ... (remaining 37135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.33: 50054 5.33 - 10.65: 134 10.65 - 15.98: 5 15.98 - 21.30: 4 21.30 - 26.63: 4 Bond angle restraints: 50201 Sorted by residual: angle pdb=" PB ATP G1001 " pdb=" O3B ATP G1001 " pdb=" PG ATP G1001 " ideal model delta sigma weight residual 139.87 113.24 26.63 1.00e+00 1.00e+00 7.09e+02 angle pdb=" PA ATP E1001 " pdb=" O3A ATP E1001 " pdb=" PB ATP E1001 " ideal model delta sigma weight residual 136.83 111.45 25.38 1.00e+00 1.00e+00 6.44e+02 angle pdb=" PB ATP I1001 " pdb=" O3B ATP I1001 " pdb=" PG ATP I1001 " ideal model delta sigma weight residual 139.87 115.60 24.27 1.00e+00 1.00e+00 5.89e+02 angle pdb=" PA ATP C1001 " pdb=" O3A ATP C1001 " pdb=" PB ATP C1001 " ideal model delta sigma weight residual 136.83 114.55 22.28 1.00e+00 1.00e+00 4.96e+02 angle pdb=" PB ATP E1001 " pdb=" O3B ATP E1001 " pdb=" PG ATP E1001 " ideal model delta sigma weight residual 139.87 120.32 19.55 1.00e+00 1.00e+00 3.82e+02 ... (remaining 50196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 20329 17.96 - 35.91: 1987 35.91 - 53.87: 340 53.87 - 71.82: 77 71.82 - 89.78: 21 Dihedral angle restraints: 22754 sinusoidal: 9519 harmonic: 13235 Sorted by residual: dihedral pdb=" C THR A 174 " pdb=" N THR A 174 " pdb=" CA THR A 174 " pdb=" CB THR A 174 " ideal model delta harmonic sigma weight residual -122.00 -137.01 15.01 0 2.50e+00 1.60e-01 3.61e+01 dihedral pdb=" C LEU C 204 " pdb=" N LEU C 204 " pdb=" CA LEU C 204 " pdb=" CB LEU C 204 " ideal model delta harmonic sigma weight residual -122.60 -109.86 -12.74 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C ASP A 507 " pdb=" N ASP A 507 " pdb=" CA ASP A 507 " pdb=" CB ASP A 507 " ideal model delta harmonic sigma weight residual -122.60 -134.87 12.27 0 2.50e+00 1.60e-01 2.41e+01 ... (remaining 22751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 5292 0.098 - 0.197: 399 0.197 - 0.295: 32 0.295 - 0.393: 3 0.393 - 0.491: 2 Chirality restraints: 5728 Sorted by residual: chirality pdb=" CA LEU C 204 " pdb=" N LEU C 204 " pdb=" C LEU C 204 " pdb=" CB LEU C 204 " both_signs ideal model delta sigma weight residual False 2.51 3.00 -0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" CA THR A 174 " pdb=" N THR A 174 " pdb=" C THR A 174 " pdb=" CB THR A 174 " both_signs ideal model delta sigma weight residual False 2.53 2.09 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ASP A 507 " pdb=" N ASP A 507 " pdb=" C ASP A 507 " pdb=" CB ASP A 507 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 5725 not shown) Planarity restraints: 6278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 171 " 0.021 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C ILE E 171 " -0.076 2.00e-02 2.50e+03 pdb=" O ILE E 171 " 0.028 2.00e-02 2.50e+03 pdb=" N GLU E 172 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 173 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C GLU A 173 " -0.063 2.00e-02 2.50e+03 pdb=" O GLU A 173 " 0.023 2.00e-02 2.50e+03 pdb=" N THR A 174 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 173 " 0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C GLU E 173 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU E 173 " 0.023 2.00e-02 2.50e+03 pdb=" N THR E 174 " 0.021 2.00e-02 2.50e+03 ... (remaining 6275 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 508 2.61 - 3.18: 33790 3.18 - 3.75: 55823 3.75 - 4.33: 76379 4.33 - 4.90: 121915 Nonbonded interactions: 288415 Sorted by model distance: nonbonded pdb=" O LEU I 770 " pdb=" CD1 LEU I 770 " model vdw 2.033 3.460 nonbonded pdb=" O SER A 640 " pdb=" OG SER A 640 " model vdw 2.143 3.040 nonbonded pdb=" N GLU A 172 " pdb=" OE1 GLU A 172 " model vdw 2.161 3.120 nonbonded pdb=" O GLY E 351 " pdb=" NE2 GLN E 354 " model vdw 2.198 3.120 nonbonded pdb=" O SER C 189 " pdb=" OG SER C 189 " model vdw 2.200 3.040 ... (remaining 288410 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.530 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.006 0.079 37140 Z= 0.351 Angle : 0.955 26.630 50201 Z= 0.615 Chirality : 0.055 0.491 5728 Planarity : 0.006 0.094 6278 Dihedral : 14.509 89.776 14172 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.94 % Favored : 90.02 % Rotamer: Outliers : 1.27 % Allowed : 1.45 % Favored : 97.28 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.13), residues: 4488 helix: 0.27 (0.13), residues: 1683 sheet: -1.32 (0.25), residues: 450 loop : -1.61 (0.13), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 119 TYR 0.025 0.002 TYR E 74 PHE 0.025 0.002 PHE G 201 TRP 0.037 0.002 TRP G 285 HIS 0.007 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00624 (37140) covalent geometry : angle 0.95499 (50201) hydrogen bonds : bond 0.18687 ( 1262) hydrogen bonds : angle 6.58101 ( 3597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 467 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.7703 (p0) cc_final: 0.7239 (p0) REVERT: A 263 TYR cc_start: 0.8429 (m-80) cc_final: 0.7666 (m-80) REVERT: A 346 PHE cc_start: 0.4808 (m-10) cc_final: 0.4552 (m-10) REVERT: A 843 MET cc_start: 0.5683 (tpp) cc_final: 0.5419 (tpp) REVERT: B 245 LYS cc_start: 0.6899 (mmpt) cc_final: 0.6519 (mmtt) REVERT: C 413 MET cc_start: 0.9060 (ppp) cc_final: 0.8821 (tmm) REVERT: C 614 LEU cc_start: 0.8880 (tt) cc_final: 0.8638 (mm) REVERT: C 843 MET cc_start: 0.7247 (mmm) cc_final: 0.7036 (mmm) REVERT: E 173 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7669 (tp30) REVERT: E 854 ARG cc_start: 0.6418 (mmp80) cc_final: 0.6202 (mmp80) REVERT: G 34 GLU cc_start: 0.7769 (mp0) cc_final: 0.7553 (mp0) REVERT: G 529 MET cc_start: 0.8058 (mmm) cc_final: 0.6365 (tpp) REVERT: G 687 LEU cc_start: 0.9104 (mm) cc_final: 0.8632 (tt) REVERT: I 31 LYS cc_start: 0.8523 (ptpp) cc_final: 0.8323 (ptpp) REVERT: I 158 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7664 (ttp) REVERT: I 416 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8635 (mm) REVERT: I 637 LEU cc_start: 0.8945 (mm) cc_final: 0.8707 (mt) REVERT: I 645 ARG cc_start: 0.7577 (ttp-110) cc_final: 0.7366 (ttp-110) outliers start: 52 outliers final: 29 residues processed: 513 average time/residue: 0.2269 time to fit residues: 184.0446 Evaluate side-chains 361 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 329 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 277 TYR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 175 ARG Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 375 ILE Chi-restraints excluded: chain I residue 416 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.0020 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 0.1980 chunk 424 optimal weight: 3.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN B 263 GLN C 44 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 HIS E 477 ASN E 610 HIS G 354 GLN G 610 HIS I 597 ASN I 875 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.098119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.073692 restraints weight = 119312.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.075561 restraints weight = 63172.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.076768 restraints weight = 42843.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.077540 restraints weight = 33594.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.078024 restraints weight = 28810.109| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37140 Z= 0.135 Angle : 0.669 13.163 50201 Z= 0.338 Chirality : 0.045 0.145 5728 Planarity : 0.004 0.055 6278 Dihedral : 8.531 86.750 5139 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.98 % Favored : 92.00 % Rotamer: Outliers : 1.67 % Allowed : 9.40 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.13), residues: 4488 helix: 0.40 (0.13), residues: 1734 sheet: -1.41 (0.24), residues: 465 loop : -1.62 (0.13), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 552 TYR 0.028 0.001 TYR E 654 PHE 0.017 0.001 PHE A 781 TRP 0.034 0.001 TRP E 188 HIS 0.007 0.001 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00292 (37140) covalent geometry : angle 0.66944 (50201) hydrogen bonds : bond 0.04998 ( 1262) hydrogen bonds : angle 4.91580 ( 3597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 414 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7264 (pm20) cc_final: 0.6848 (pm20) REVERT: A 260 ASP cc_start: 0.7570 (p0) cc_final: 0.7184 (p0) REVERT: A 263 TYR cc_start: 0.8423 (m-80) cc_final: 0.7730 (m-80) REVERT: B 245 LYS cc_start: 0.6874 (mmpt) cc_final: 0.6565 (mmtt) REVERT: B 345 LYS cc_start: 0.8751 (mppt) cc_final: 0.8482 (mptt) REVERT: B 409 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8538 (mtmt) REVERT: C 126 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6857 (tm-30) REVERT: C 136 GLU cc_start: 0.8217 (pm20) cc_final: 0.7753 (pm20) REVERT: C 413 MET cc_start: 0.9067 (ppp) cc_final: 0.8734 (tmm) REVERT: C 616 MET cc_start: 0.7562 (tmm) cc_final: 0.7348 (tmm) REVERT: C 645 ARG cc_start: 0.7360 (ttp-170) cc_final: 0.7109 (ttp-170) REVERT: G 25 LEU cc_start: 0.8017 (tp) cc_final: 0.7731 (tp) REVERT: G 27 LYS cc_start: 0.8735 (mmtm) cc_final: 0.8498 (mmtm) REVERT: G 28 LYS cc_start: 0.8777 (tmtt) cc_final: 0.8508 (tptp) REVERT: G 687 LEU cc_start: 0.9163 (mm) cc_final: 0.8613 (tt) REVERT: G 873 MET cc_start: 0.3490 (tmm) cc_final: 0.3270 (tmm) REVERT: I 31 LYS cc_start: 0.8574 (ptpp) cc_final: 0.8247 (ptpp) REVERT: I 175 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7644 (ptt-90) REVERT: I 548 VAL cc_start: 0.6518 (t) cc_final: 0.6234 (t) outliers start: 68 outliers final: 35 residues processed: 462 average time/residue: 0.2214 time to fit residues: 162.6214 Evaluate side-chains 379 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 342 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 735 CYS Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 175 ARG Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 715 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 24 optimal weight: 6.9990 chunk 424 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 142 optimal weight: 0.1980 chunk 300 optimal weight: 0.0070 chunk 393 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 448 optimal weight: 0.0050 chunk 247 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 overall best weight: 0.6214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 610 HIS G 354 GLN I 68 ASN I 517 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.098421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.073906 restraints weight = 119708.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075810 restraints weight = 64001.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.077028 restraints weight = 43413.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.077816 restraints weight = 33985.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.078311 restraints weight = 29083.900| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37140 Z= 0.118 Angle : 0.607 10.972 50201 Z= 0.305 Chirality : 0.043 0.139 5728 Planarity : 0.004 0.056 6278 Dihedral : 7.712 89.692 5096 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.13 % Allowed : 13.01 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.13), residues: 4488 helix: 0.61 (0.13), residues: 1734 sheet: -1.24 (0.25), residues: 450 loop : -1.58 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 645 TYR 0.024 0.001 TYR E 654 PHE 0.013 0.001 PHE I 341 TRP 0.031 0.001 TRP E 188 HIS 0.006 0.001 HIS I 191 Details of bonding type rmsd covalent geometry : bond 0.00258 (37140) covalent geometry : angle 0.60697 (50201) hydrogen bonds : bond 0.04429 ( 1262) hydrogen bonds : angle 4.55282 ( 3597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 387 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.7499 (p0) cc_final: 0.7165 (p0) REVERT: A 263 TYR cc_start: 0.8480 (m-80) cc_final: 0.7795 (m-80) REVERT: A 379 SER cc_start: 0.8691 (m) cc_final: 0.8158 (p) REVERT: A 478 GLU cc_start: 0.7184 (tp30) cc_final: 0.6921 (tp30) REVERT: B 245 LYS cc_start: 0.6876 (mmpt) cc_final: 0.6601 (mmtt) REVERT: B 327 MET cc_start: 0.5408 (tpt) cc_final: 0.5203 (tpt) REVERT: C 37 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.8976 (tp) REVERT: C 616 MET cc_start: 0.7471 (tmm) cc_final: 0.7251 (tmm) REVERT: C 645 ARG cc_start: 0.7345 (ttp-170) cc_final: 0.7089 (ttp-170) REVERT: E 690 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8121 (pp) REVERT: G 39 GLU cc_start: 0.8498 (tt0) cc_final: 0.8296 (tt0) REVERT: G 71 GLU cc_start: 0.8296 (tp30) cc_final: 0.7854 (tp30) REVERT: G 158 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8338 (tpt) REVERT: G 843 MET cc_start: 0.5463 (mmm) cc_final: 0.5189 (mmm) REVERT: I 27 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8305 (mmmt) REVERT: I 31 LYS cc_start: 0.8616 (ptpp) cc_final: 0.8122 (ptpp) REVERT: I 132 LYS cc_start: 0.8896 (mptt) cc_final: 0.8556 (mmmt) REVERT: I 175 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8589 (ptt-90) REVERT: I 548 VAL cc_start: 0.6558 (t) cc_final: 0.6329 (t) outliers start: 87 outliers final: 45 residues processed: 452 average time/residue: 0.2190 time to fit residues: 158.6035 Evaluate side-chains 396 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 347 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 175 ARG Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 715 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 190 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 358 optimal weight: 0.9990 chunk 284 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 324 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 359 optimal weight: 7.9990 chunk 365 optimal weight: 0.2980 chunk 333 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN E 610 HIS G 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.097039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.072462 restraints weight = 120174.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074301 restraints weight = 64339.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075504 restraints weight = 43813.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.076265 restraints weight = 34328.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.076744 restraints weight = 29542.072| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37140 Z= 0.141 Angle : 0.604 11.886 50201 Z= 0.305 Chirality : 0.043 0.198 5728 Planarity : 0.004 0.056 6278 Dihedral : 7.414 88.366 5092 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.72 % Allowed : 14.92 % Favored : 82.37 % 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: -0.98 (0.13), residues: 4488 helix: 0.68 (0.13), residues: 1739 sheet: -1.38 (0.25), residues: 460 loop : -1.57 (0.13), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 645 TYR 0.025 0.001 TYR E 654 PHE 0.020 0.001 PHE A 781 TRP 0.014 0.001 TRP B 210 HIS 0.005 0.001 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00327 (37140) covalent geometry : angle 0.60410 (50201) hydrogen bonds : bond 0.04246 ( 1262) hydrogen bonds : angle 4.38648 ( 3597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 364 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8157 (ptt90) REVERT: A 260 ASP cc_start: 0.7646 (p0) cc_final: 0.7313 (p0) REVERT: A 263 TYR cc_start: 0.8591 (m-80) cc_final: 0.7991 (m-80) REVERT: B 245 LYS cc_start: 0.6958 (mmpt) cc_final: 0.6619 (mmtt) REVERT: B 327 MET cc_start: 0.5299 (tpt) cc_final: 0.5068 (tpt) REVERT: B 345 LYS cc_start: 0.8964 (pttp) cc_final: 0.8488 (mmtm) REVERT: C 37 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.8992 (tp) REVERT: C 645 ARG cc_start: 0.7303 (ttp-170) cc_final: 0.7061 (ttp-170) REVERT: E 30 ARG cc_start: 0.8369 (mmt90) cc_final: 0.8168 (mtt90) REVERT: E 177 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8766 (tmmm) REVERT: E 690 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8176 (pp) REVERT: G 71 GLU cc_start: 0.8299 (tp30) cc_final: 0.7783 (tp30) REVERT: G 133 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: G 158 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8322 (tpt) REVERT: G 687 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8568 (tt) REVERT: I 27 LYS cc_start: 0.8620 (mmmt) cc_final: 0.8386 (mmmt) REVERT: I 31 LYS cc_start: 0.8657 (ptpp) cc_final: 0.8420 (ptpp) REVERT: I 44 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8206 (mp10) REVERT: I 132 LYS cc_start: 0.8942 (mptt) cc_final: 0.8611 (mmmt) REVERT: I 548 VAL cc_start: 0.6468 (t) cc_final: 0.6139 (t) outliers start: 111 outliers final: 71 residues processed: 446 average time/residue: 0.2227 time to fit residues: 158.9494 Evaluate side-chains 419 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 340 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 577 LYS Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 133 GLN Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 721 LEU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 44 GLN Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 707 MET Chi-restraints excluded: chain I residue 715 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 309 optimal weight: 4.9990 chunk 46 optimal weight: 0.1980 chunk 348 optimal weight: 0.9980 chunk 322 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 407 ASN E 502 HIS G 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.095599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.070986 restraints weight = 119729.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.072832 restraints weight = 64360.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.074013 restraints weight = 43709.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.074759 restraints weight = 34334.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.075220 restraints weight = 29599.688| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 37140 Z= 0.183 Angle : 0.635 9.788 50201 Z= 0.322 Chirality : 0.045 0.182 5728 Planarity : 0.004 0.059 6278 Dihedral : 7.372 87.056 5085 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 3.28 % Allowed : 15.67 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.13), residues: 4488 helix: 0.63 (0.13), residues: 1769 sheet: -1.45 (0.25), residues: 460 loop : -1.61 (0.13), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 645 TYR 0.027 0.002 TYR E 654 PHE 0.017 0.001 PHE A 438 TRP 0.015 0.001 TRP I 285 HIS 0.006 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00429 (37140) covalent geometry : angle 0.63546 (50201) hydrogen bonds : bond 0.04518 ( 1262) hydrogen bonds : angle 4.37021 ( 3597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 356 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.7767 (p0) cc_final: 0.7478 (p0) REVERT: A 263 TYR cc_start: 0.8546 (m-80) cc_final: 0.8060 (m-80) REVERT: A 478 GLU cc_start: 0.7333 (tp30) cc_final: 0.7026 (tp30) REVERT: B 245 LYS cc_start: 0.6901 (mmpt) cc_final: 0.6571 (mmtt) REVERT: C 37 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9023 (tp) REVERT: C 407 ASN cc_start: 0.6067 (m-40) cc_final: 0.5809 (m110) REVERT: C 645 ARG cc_start: 0.7281 (ttp-170) cc_final: 0.7035 (ttp-170) REVERT: C 648 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7129 (mpp) REVERT: E 30 ARG cc_start: 0.8331 (mmt90) cc_final: 0.7989 (mmm-85) REVERT: E 177 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8777 (tmmm) REVERT: E 690 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8395 (pp) REVERT: G 71 GLU cc_start: 0.8379 (tp30) cc_final: 0.7909 (tp30) REVERT: G 133 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8005 (mp10) REVERT: G 158 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8281 (tpt) REVERT: G 183 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8369 (t) REVERT: G 266 ASP cc_start: 0.7993 (m-30) cc_final: 0.7775 (m-30) REVERT: G 554 GLU cc_start: 0.7407 (pm20) cc_final: 0.7062 (pm20) REVERT: G 687 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8612 (tt) REVERT: I 27 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8363 (mmmt) REVERT: I 31 LYS cc_start: 0.8656 (ptpp) cc_final: 0.8439 (ptpp) REVERT: I 548 VAL cc_start: 0.6543 (OUTLIER) cc_final: 0.6204 (t) outliers start: 134 outliers final: 89 residues processed: 460 average time/residue: 0.2167 time to fit residues: 160.6607 Evaluate side-chains 429 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 331 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 509 ILE Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 626 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 133 GLN Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 639 TRP Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 721 LEU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 440 GLU Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 707 MET Chi-restraints excluded: chain I residue 715 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 436 optimal weight: 2.9990 chunk 426 optimal weight: 9.9990 chunk 384 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 392 optimal weight: 2.9990 chunk 70 optimal weight: 0.0470 chunk 272 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 254 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN G 130 GLN G 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.097322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072877 restraints weight = 119761.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.074796 restraints weight = 63894.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.076013 restraints weight = 43163.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076805 restraints weight = 33815.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077288 restraints weight = 28926.256| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37140 Z= 0.113 Angle : 0.602 11.130 50201 Z= 0.301 Chirality : 0.043 0.232 5728 Planarity : 0.004 0.074 6278 Dihedral : 7.041 88.687 5085 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.11 % Allowed : 16.63 % Favored : 80.26 % 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: -0.95 (0.13), residues: 4488 helix: 0.72 (0.13), residues: 1774 sheet: -1.46 (0.25), residues: 460 loop : -1.58 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 552 TYR 0.027 0.001 TYR E 654 PHE 0.022 0.001 PHE E 341 TRP 0.013 0.001 TRP E 188 HIS 0.004 0.001 HIS E 402 Details of bonding type rmsd covalent geometry : bond 0.00251 (37140) covalent geometry : angle 0.60160 (50201) hydrogen bonds : bond 0.03985 ( 1262) hydrogen bonds : angle 4.22184 ( 3597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 361 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.7688 (p0) cc_final: 0.7344 (p0) REVERT: A 263 TYR cc_start: 0.8485 (m-80) cc_final: 0.8023 (m-80) REVERT: A 478 GLU cc_start: 0.7314 (tp30) cc_final: 0.7008 (tp30) REVERT: B 245 LYS cc_start: 0.6885 (mmpt) cc_final: 0.6547 (mmtt) REVERT: B 345 LYS cc_start: 0.8965 (pttp) cc_final: 0.8437 (mmtm) REVERT: C 37 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.8980 (tp) REVERT: C 407 ASN cc_start: 0.6029 (m-40) cc_final: 0.5684 (m110) REVERT: C 645 ARG cc_start: 0.7264 (ttp-170) cc_final: 0.6968 (ttp-170) REVERT: C 648 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7142 (mpp) REVERT: E 177 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8756 (tmmm) REVERT: E 552 ARG cc_start: 0.7271 (mmm160) cc_final: 0.7036 (mmm160) REVERT: E 690 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8290 (pp) REVERT: G 71 GLU cc_start: 0.8476 (tp30) cc_final: 0.7959 (tp30) REVERT: G 158 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8281 (tpt) REVERT: G 183 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8021 (t) REVERT: G 529 MET cc_start: 0.8017 (mmm) cc_final: 0.6256 (tpp) REVERT: G 556 MET cc_start: 0.8752 (tpp) cc_final: 0.8546 (tpp) REVERT: G 687 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8573 (tt) REVERT: G 854 ARG cc_start: 0.3556 (tpt90) cc_final: 0.1998 (mmp80) REVERT: I 27 LYS cc_start: 0.8566 (mmmt) cc_final: 0.8313 (mmmt) REVERT: I 31 LYS cc_start: 0.8632 (ptpp) cc_final: 0.8399 (ptpp) REVERT: I 548 VAL cc_start: 0.6459 (OUTLIER) cc_final: 0.6128 (t) outliers start: 127 outliers final: 80 residues processed: 455 average time/residue: 0.2163 time to fit residues: 159.4382 Evaluate side-chains 428 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 340 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 484 MET Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 577 LYS Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 626 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 639 TRP Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 721 LEU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 363 ILE Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 466 ILE Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 707 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 52 optimal weight: 4.9990 chunk 226 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 320 optimal weight: 0.8980 chunk 345 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 303 optimal weight: 0.5980 chunk 364 optimal weight: 3.9990 chunk 427 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS C 130 GLN G 130 GLN I 464 GLN I 517 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.097265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.072908 restraints weight = 120034.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.074817 restraints weight = 63765.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.076038 restraints weight = 43004.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076804 restraints weight = 33521.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077298 restraints weight = 28730.962| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37140 Z= 0.117 Angle : 0.607 10.571 50201 Z= 0.303 Chirality : 0.043 0.191 5728 Planarity : 0.004 0.086 6278 Dihedral : 6.883 88.060 5081 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.77 % Allowed : 17.22 % Favored : 80.01 % 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: -0.91 (0.13), residues: 4488 helix: 0.79 (0.13), residues: 1774 sheet: -1.47 (0.25), residues: 460 loop : -1.58 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 552 TYR 0.026 0.001 TYR E 654 PHE 0.031 0.001 PHE E 683 TRP 0.015 0.001 TRP E 188 HIS 0.004 0.001 HIS E 402 Details of bonding type rmsd covalent geometry : bond 0.00267 (37140) covalent geometry : angle 0.60720 (50201) hydrogen bonds : bond 0.03829 ( 1262) hydrogen bonds : angle 4.14908 ( 3597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 361 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.7676 (p0) cc_final: 0.7299 (p0) REVERT: A 263 TYR cc_start: 0.8510 (m-80) cc_final: 0.8107 (m-80) REVERT: A 379 SER cc_start: 0.8656 (m) cc_final: 0.8120 (p) REVERT: B 245 LYS cc_start: 0.6836 (mmpt) cc_final: 0.6588 (mmtt) REVERT: B 345 LYS cc_start: 0.8944 (pttp) cc_final: 0.8417 (mmtm) REVERT: C 37 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.8981 (tp) REVERT: C 130 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7543 (mp10) REVERT: C 648 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7168 (mpp) REVERT: E 126 GLU cc_start: 0.8218 (tp30) cc_final: 0.7823 (tp30) REVERT: E 177 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8751 (tmmm) REVERT: E 313 VAL cc_start: 0.9559 (OUTLIER) cc_final: 0.9328 (p) REVERT: E 552 ARG cc_start: 0.7238 (mmm160) cc_final: 0.7015 (mmm160) REVERT: E 690 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8296 (pp) REVERT: G 71 GLU cc_start: 0.8466 (tp30) cc_final: 0.7996 (tp30) REVERT: G 158 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8276 (tpt) REVERT: G 183 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8042 (t) REVERT: G 529 MET cc_start: 0.7666 (mmm) cc_final: 0.6353 (tpp) REVERT: G 556 MET cc_start: 0.8731 (tpp) cc_final: 0.8514 (tpp) REVERT: G 687 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8559 (tt) REVERT: G 854 ARG cc_start: 0.3557 (tpt90) cc_final: 0.1969 (mmp80) REVERT: I 27 LYS cc_start: 0.8582 (mmmt) cc_final: 0.8313 (mmmt) REVERT: I 31 LYS cc_start: 0.8640 (ptpp) cc_final: 0.8423 (ptpp) REVERT: I 388 LYS cc_start: 0.3815 (OUTLIER) cc_final: 0.3189 (ptmm) REVERT: I 548 VAL cc_start: 0.6454 (OUTLIER) cc_final: 0.6136 (t) REVERT: I 553 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6537 (ptp) outliers start: 113 outliers final: 86 residues processed: 448 average time/residue: 0.2113 time to fit residues: 153.8861 Evaluate side-chains 441 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 343 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 577 LYS Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 626 THR Chi-restraints excluded: chain E residue 656 MET Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 581 VAL Chi-restraints excluded: chain G residue 598 LEU Chi-restraints excluded: chain G residue 639 TRP Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 721 LEU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 392 GLU Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 466 ILE Chi-restraints excluded: chain I residue 484 MET Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 681 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 137 optimal weight: 2.9990 chunk 269 optimal weight: 9.9990 chunk 309 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 439 optimal weight: 8.9990 chunk 202 optimal weight: 0.3980 chunk 271 optimal weight: 9.9990 chunk 397 optimal weight: 0.3980 chunk 342 optimal weight: 0.9990 chunk 416 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 432 HIS C 130 GLN I 517 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.097103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.072766 restraints weight = 119902.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.074654 restraints weight = 63769.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.075871 restraints weight = 43063.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.076642 restraints weight = 33616.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.077101 restraints weight = 28765.434| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37140 Z= 0.125 Angle : 0.621 13.863 50201 Z= 0.308 Chirality : 0.043 0.190 5728 Planarity : 0.004 0.058 6278 Dihedral : 6.838 87.030 5081 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.87 % Allowed : 17.66 % Favored : 79.48 % 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: -0.89 (0.13), residues: 4488 helix: 0.83 (0.13), residues: 1774 sheet: -1.50 (0.25), residues: 460 loop : -1.59 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 552 TYR 0.027 0.001 TYR E 654 PHE 0.026 0.001 PHE E 683 TRP 0.016 0.001 TRP E 188 HIS 0.005 0.001 HIS B 432 Details of bonding type rmsd covalent geometry : bond 0.00289 (37140) covalent geometry : angle 0.62068 (50201) hydrogen bonds : bond 0.03850 ( 1262) hydrogen bonds : angle 4.11760 ( 3597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 351 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.7677 (p0) cc_final: 0.7322 (p0) REVERT: A 263 TYR cc_start: 0.8518 (m-80) cc_final: 0.8122 (m-80) REVERT: A 379 SER cc_start: 0.8622 (m) cc_final: 0.8081 (p) REVERT: A 478 GLU cc_start: 0.7097 (tp30) cc_final: 0.6850 (tp30) REVERT: B 245 LYS cc_start: 0.6844 (mmpt) cc_final: 0.6596 (mmtt) REVERT: B 345 LYS cc_start: 0.8958 (pttp) cc_final: 0.8428 (mmtm) REVERT: C 37 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.8999 (tp) REVERT: C 126 GLU cc_start: 0.7773 (tp30) cc_final: 0.7427 (tp30) REVERT: C 648 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7183 (mpp) REVERT: C 770 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8938 (pp) REVERT: E 177 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8757 (tmmm) REVERT: E 552 ARG cc_start: 0.7294 (mmm160) cc_final: 0.7027 (mmm160) REVERT: E 648 MET cc_start: 0.8602 (mtt) cc_final: 0.8382 (mtt) REVERT: E 690 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8313 (pp) REVERT: G 27 LYS cc_start: 0.8327 (mppt) cc_final: 0.7886 (mppt) REVERT: G 71 GLU cc_start: 0.8454 (tp30) cc_final: 0.7996 (tp30) REVERT: G 158 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8277 (tpt) REVERT: G 183 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8027 (t) REVERT: G 687 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8562 (tt) REVERT: G 854 ARG cc_start: 0.3649 (tpt90) cc_final: 0.2059 (mmp80) REVERT: I 27 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8323 (mmmt) REVERT: I 31 LYS cc_start: 0.8646 (ptpp) cc_final: 0.8428 (ptpp) REVERT: I 388 LYS cc_start: 0.3857 (OUTLIER) cc_final: 0.3258 (ptmm) REVERT: I 548 VAL cc_start: 0.6460 (OUTLIER) cc_final: 0.6113 (t) REVERT: I 553 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.6873 (ptm) outliers start: 117 outliers final: 89 residues processed: 438 average time/residue: 0.2180 time to fit residues: 154.9484 Evaluate side-chains 440 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 340 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 484 MET Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 577 LYS Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 626 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 581 VAL Chi-restraints excluded: chain G residue 598 LEU Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 721 LEU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 392 GLU Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 484 MET Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 707 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 284 optimal weight: 7.9990 chunk 358 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 205 optimal weight: 0.7980 chunk 404 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 417 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 407 optimal weight: 0.4980 chunk 76 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN B 432 HIS G 130 GLN I 133 GLN I 517 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.097583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073244 restraints weight = 120271.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.075145 restraints weight = 63741.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.076363 restraints weight = 42892.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.077141 restraints weight = 33526.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.077624 restraints weight = 28671.565| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37140 Z= 0.115 Angle : 0.632 13.802 50201 Z= 0.311 Chirality : 0.043 0.202 5728 Planarity : 0.004 0.079 6278 Dihedral : 6.721 84.708 5080 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.57 % Allowed : 18.42 % Favored : 79.01 % 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: -0.87 (0.13), residues: 4488 helix: 0.86 (0.13), residues: 1774 sheet: -1.52 (0.24), residues: 460 loop : -1.57 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 552 TYR 0.027 0.001 TYR E 654 PHE 0.025 0.001 PHE E 683 TRP 0.041 0.001 TRP E 188 HIS 0.007 0.001 HIS B 432 Details of bonding type rmsd covalent geometry : bond 0.00262 (37140) covalent geometry : angle 0.63158 (50201) hydrogen bonds : bond 0.03696 ( 1262) hydrogen bonds : angle 4.07360 ( 3597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 361 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.7667 (p0) cc_final: 0.7301 (p0) REVERT: A 263 TYR cc_start: 0.8493 (m-80) cc_final: 0.8153 (m-80) REVERT: A 478 GLU cc_start: 0.7129 (tp30) cc_final: 0.6856 (tp30) REVERT: B 245 LYS cc_start: 0.6844 (mmpt) cc_final: 0.6593 (mmtt) REVERT: B 513 GLU cc_start: 0.5535 (pt0) cc_final: 0.5029 (tm-30) REVERT: C 37 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.8982 (tp) REVERT: C 648 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7187 (mpp) REVERT: C 770 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8944 (pp) REVERT: C 876 LEU cc_start: 0.6993 (mp) cc_final: 0.6712 (tt) REVERT: E 177 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8750 (tmmm) REVERT: E 552 ARG cc_start: 0.7311 (mmm160) cc_final: 0.7006 (mmm160) REVERT: E 690 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8360 (pp) REVERT: G 71 GLU cc_start: 0.8419 (tp30) cc_final: 0.8033 (tp30) REVERT: G 133 GLN cc_start: 0.8599 (mp10) cc_final: 0.8079 (mp10) REVERT: G 158 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8263 (tpt) REVERT: G 183 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7931 (t) REVERT: G 529 MET cc_start: 0.7958 (mmm) cc_final: 0.6291 (tpp) REVERT: G 687 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8536 (tt) REVERT: G 854 ARG cc_start: 0.3602 (tpt90) cc_final: 0.2025 (mmp80) REVERT: I 27 LYS cc_start: 0.8582 (mmmt) cc_final: 0.8332 (mmmt) REVERT: I 388 LYS cc_start: 0.3729 (OUTLIER) cc_final: 0.3136 (ptmm) REVERT: I 548 VAL cc_start: 0.6428 (OUTLIER) cc_final: 0.6077 (t) REVERT: I 738 GLU cc_start: 0.6624 (mm-30) cc_final: 0.6304 (tp30) outliers start: 105 outliers final: 86 residues processed: 445 average time/residue: 0.2144 time to fit residues: 154.7441 Evaluate side-chains 439 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 343 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 577 LYS Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 626 THR Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 581 VAL Chi-restraints excluded: chain G residue 598 LEU Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 721 LEU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 392 GLU Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 484 MET Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 707 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 118 optimal weight: 9.9990 chunk 259 optimal weight: 5.9990 chunk 319 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 448 optimal weight: 0.0770 chunk 431 optimal weight: 7.9990 chunk 400 optimal weight: 0.0970 chunk 124 optimal weight: 4.9990 chunk 223 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 ASN G 130 GLN G 531 ASN I 133 GLN I 517 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.098192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.073924 restraints weight = 120219.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075857 restraints weight = 63499.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.077081 restraints weight = 42661.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077868 restraints weight = 33248.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.078349 restraints weight = 28447.120| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 37140 Z= 0.110 Angle : 0.639 13.523 50201 Z= 0.314 Chirality : 0.043 0.209 5728 Planarity : 0.004 0.102 6278 Dihedral : 6.596 81.897 5079 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.45 % Allowed : 19.03 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.13), residues: 4488 helix: 0.87 (0.13), residues: 1768 sheet: -1.51 (0.24), residues: 460 loop : -1.56 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG C 552 TYR 0.024 0.001 TYR E 654 PHE 0.025 0.001 PHE E 683 TRP 0.017 0.001 TRP E 188 HIS 0.003 0.000 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00247 (37140) covalent geometry : angle 0.63939 (50201) hydrogen bonds : bond 0.03567 ( 1262) hydrogen bonds : angle 4.04551 ( 3597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 375 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.7619 (p0) cc_final: 0.7214 (p0) REVERT: A 263 TYR cc_start: 0.8462 (m-80) cc_final: 0.8104 (m-80) REVERT: A 478 GLU cc_start: 0.7147 (tp30) cc_final: 0.6880 (tp30) REVERT: B 245 LYS cc_start: 0.6784 (mmpt) cc_final: 0.6535 (mmtt) REVERT: B 299 LYS cc_start: 0.9167 (pttt) cc_final: 0.8874 (pttt) REVERT: B 345 LYS cc_start: 0.8967 (pttp) cc_final: 0.8334 (mmtm) REVERT: B 513 GLU cc_start: 0.5522 (pt0) cc_final: 0.4940 (tm-30) REVERT: C 648 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7181 (mpp) REVERT: C 770 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8951 (pp) REVERT: E 177 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8751 (tmmm) REVERT: E 552 ARG cc_start: 0.7334 (mmm160) cc_final: 0.7013 (mmm160) REVERT: E 690 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8261 (pp) REVERT: E 707 MET cc_start: 0.6751 (pmm) cc_final: 0.5146 (ptp) REVERT: G 71 GLU cc_start: 0.8399 (tp30) cc_final: 0.8000 (tp30) REVERT: G 158 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8268 (tpt) REVERT: G 183 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.7954 (t) REVERT: G 529 MET cc_start: 0.7987 (mmm) cc_final: 0.6399 (tpp) REVERT: G 535 LYS cc_start: 0.6954 (pptt) cc_final: 0.5776 (pptt) REVERT: G 687 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8497 (tt) REVERT: G 854 ARG cc_start: 0.3526 (tpt90) cc_final: 0.2006 (mmp80) REVERT: G 873 MET cc_start: 0.3967 (tmm) cc_final: 0.3328 (tmm) REVERT: I 31 LYS cc_start: 0.8705 (ptpp) cc_final: 0.8261 (ptpp) REVERT: I 388 LYS cc_start: 0.3414 (OUTLIER) cc_final: 0.2796 (ptmm) REVERT: I 548 VAL cc_start: 0.6428 (OUTLIER) cc_final: 0.6093 (t) REVERT: I 612 LYS cc_start: 0.7773 (mmmt) cc_final: 0.7560 (mmmt) REVERT: I 637 LEU cc_start: 0.9019 (mm) cc_final: 0.8798 (mt) REVERT: I 738 GLU cc_start: 0.6656 (mm-30) cc_final: 0.6398 (tp30) outliers start: 100 outliers final: 83 residues processed: 451 average time/residue: 0.2173 time to fit residues: 157.5609 Evaluate side-chains 450 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 358 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 484 MET Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 577 LYS Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 626 THR Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 581 VAL Chi-restraints excluded: chain G residue 598 LEU Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 719 TYR Chi-restraints excluded: chain G residue 721 LEU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 392 GLU Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 466 ILE Chi-restraints excluded: chain I residue 484 MET Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 707 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 340 optimal weight: 0.0770 chunk 161 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 247 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 270 optimal weight: 5.9990 chunk 342 optimal weight: 0.7980 chunk 220 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 362 optimal weight: 10.0000 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 432 HIS C 44 GLN G 130 GLN G 354 GLN I 68 ASN I 517 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.097272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.072901 restraints weight = 119012.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.074804 restraints weight = 63619.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.076012 restraints weight = 42886.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076794 restraints weight = 33519.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077264 restraints weight = 28642.327| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37140 Z= 0.132 Angle : 0.650 12.619 50201 Z= 0.321 Chirality : 0.044 0.199 5728 Planarity : 0.004 0.105 6278 Dihedral : 6.659 82.833 5079 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.52 % Allowed : 19.10 % Favored : 78.37 % 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: -0.87 (0.13), residues: 4488 helix: 0.86 (0.13), residues: 1768 sheet: -1.52 (0.24), residues: 460 loop : -1.57 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG C 552 TYR 0.024 0.001 TYR E 654 PHE 0.023 0.001 PHE E 683 TRP 0.022 0.001 TRP E 188 HIS 0.008 0.001 HIS B 432 Details of bonding type rmsd covalent geometry : bond 0.00308 (37140) covalent geometry : angle 0.65025 (50201) hydrogen bonds : bond 0.03738 ( 1262) hydrogen bonds : angle 4.08918 ( 3597) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7068.79 seconds wall clock time: 122 minutes 32.86 seconds (7352.86 seconds total)