Starting phenix.real_space_refine on Mon Jul 6 15:27:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xx2_33498/07_2026/7xx2_33498.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xx2_33498/07_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_33498/07_2026/7xx2_33498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xx2_33498/07_2026/7xx2_33498.map" model { file = "/net/cci-nas-00/data/ceres_data/7xx2_33498/07_2026/7xx2_33498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xx2_33498/07_2026/7xx2_33498.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xx2_33498/07_2026/7xx2_33498.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xx2_33498/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 7.21, per 1000 atoms: 0.20 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: 2.86 Conformation dependent library (CDL) restraints added in 2.0 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: 1.25 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: 7.07 Time building geometry restraints manager: 3.65 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 - 17.84: 20275 17.84 - 35.69: 1955 35.69 - 53.53: 299 53.53 - 71.37: 52 71.37 - 89.22: 18 Dihedral angle restraints: 22599 sinusoidal: 9364 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 22596 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 30.560 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 13.959 89.218 14017 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/Z covalent geometry : bond 0.00624 / 0.35 (37140) covalent geometry : angle 0.95499 / 0.61 (50201) hydrogen bonds : bond 0.18687 / 12.09 ( 1262) hydrogen bonds : angle 6.58101 / 4.60 ( 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 : 1.480 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: 0.2315 time to fit residues: 187.2428 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 : 0.963 ------------------------------------------------------------------------------- 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... A 407 ASN B 263 GLN C 44 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.097952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.073511 restraints weight = 119321.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.075381 restraints weight = 63231.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076593 restraints weight = 42875.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.077373 restraints weight = 33532.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.077822 restraints weight = 28760.593| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1337 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= 0.136 Angle : 0.669 13.121 50201 Z= 0.338 Chirality : 0.045 0.145 5728 Planarity : 0.004 0.055 6278 Dihedral : 6.355 87.792 4984 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.04 % Favored : 91.93 % Rotamer: Outliers : 1.67 % Allowed : 9.31 % Favored : 89.03 % 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: -1.19 (0.13), residues: 4488 helix: 0.41 (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 0.008 0.001 ARG A 552 TYR 0.027 0.001 TYR E 654 PHE 0.016 0.001 PHE A 781 TRP 0.032 0.001 TRP E 188 HIS 0.007 0.001 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (37140) covalent geometry : angle 0.66947 / 0.34 (50201) hydrogen bonds : bond 0.05184 / 3.39 ( 1262) hydrogen bonds : angle 4.94757 / 3.47 ( 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 476 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 408 time to evaluate : 1.146 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 136 GLU cc_start: 0.7248 (pm20) cc_final: 0.6957 (pm20) REVERT: A 260 ASP cc_start: 0.7582 (p0) cc_final: 0.7157 (p0) REVERT: A 263 TYR cc_start: 0.8427 (m-80) cc_final: 0.7667 (m-80) REVERT: A 873 MET cc_start: 0.2961 (ppp) cc_final: 0.2740 (ppp) REVERT: B 245 LYS cc_start: 0.6884 (mmpt) cc_final: 0.6574 (mmtt) REVERT: B 345 LYS cc_start: 0.8749 (mppt) cc_final: 0.8485 (mptt) REVERT: B 409 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8536 (mtmt) REVERT: C 126 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: C 136 GLU cc_start: 0.8240 (pm20) cc_final: 0.7774 (pm20) REVERT: C 413 MET cc_start: 0.9072 (ppp) cc_final: 0.8754 (tmm) REVERT: C 616 MET cc_start: 0.7567 (tmm) cc_final: 0.7355 (tmm) REVERT: C 645 ARG cc_start: 0.7370 (ttp-170) cc_final: 0.7136 (ttp-170) REVERT: E 81 ASP cc_start: 0.9007 (t0) cc_final: 0.8687 (t0) REVERT: G 27 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8519 (mmtm) REVERT: G 28 LYS cc_start: 0.8791 (tmtt) cc_final: 0.8508 (tptp) REVERT: G 687 LEU cc_start: 0.9162 (mm) cc_final: 0.8619 (tt) REVERT: G 873 MET cc_start: 0.3503 (tmm) cc_final: 0.3283 (tmm) REVERT: I 31 LYS cc_start: 0.8573 (ptpp) cc_final: 0.8245 (ptpp) REVERT: I 71 GLU cc_start: 0.8093 (tp30) cc_final: 0.7721 (tp30) REVERT: I 548 VAL cc_start: 0.6520 (t) cc_final: 0.6238 (t) outliers start: 68 outliers final: 36 residues processed: 455 average time/residue: 0.2212 time to fit residues: 159.5912 Evaluate side-chains 377 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 340 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 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 639 TRP 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: 5.9990 chunk 424 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 393 optimal weight: 0.9990 chunk 140 optimal weight: 0.0670 chunk 448 optimal weight: 8.9990 chunk 247 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 201 optimal weight: 0.7980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 359 HIS C 44 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.097272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.072686 restraints weight = 119404.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.074526 restraints weight = 63417.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075728 restraints weight = 43068.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076478 restraints weight = 33748.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.076952 restraints weight = 28953.551| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- 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 = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37140 Z= 0.140 Angle : 0.619 10.702 50201 Z= 0.313 Chirality : 0.044 0.139 5728 Planarity : 0.004 0.056 6278 Dihedral : 5.733 89.256 4941 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.25 % Allowed : 13.01 % Favored : 84.74 % 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: -1.04 (0.13), residues: 4488 helix: 0.58 (0.13), residues: 1734 sheet: -1.25 (0.25), residues: 450 loop : -1.60 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 119 TYR 0.024 0.001 TYR E 654 PHE 0.014 0.001 PHE A 438 TRP 0.030 0.001 TRP E 188 HIS 0.006 0.001 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (37140) covalent geometry : angle 0.61867 / 0.31 (50201) hydrogen bonds : bond 0.04620 / 3.04 ( 1262) hydrogen bonds : angle 4.58218 / 3.22 ( 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 472 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 380 time to evaluate : 1.119 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: 0.7610 (p0) cc_final: 0.7315 (p0) REVERT: A 263 TYR cc_start: 0.8530 (m-80) cc_final: 0.7881 (m-80) REVERT: A 478 GLU cc_start: 0.7203 (tp30) cc_final: 0.6942 (tp30) REVERT: B 245 LYS cc_start: 0.6908 (mmpt) cc_final: 0.6634 (mmtt) REVERT: B 327 MET cc_start: 0.5359 (tpt) cc_final: 0.5157 (tpt) REVERT: C 37 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.8979 (tp) REVERT: C 43 MET cc_start: 0.8615 (mtm) cc_final: 0.8409 (mtp) REVERT: C 616 MET cc_start: 0.7436 (tmm) cc_final: 0.7231 (tmm) REVERT: C 645 ARG cc_start: 0.7333 (ttp-170) cc_final: 0.7085 (ttp-170) REVERT: E 648 MET cc_start: 0.8536 (mmm) cc_final: 0.8310 (mtt) REVERT: E 690 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8180 (pp) REVERT: G 71 GLU cc_start: 0.8330 (tp30) cc_final: 0.7874 (tp30) REVERT: G 158 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8331 (tpt) REVERT: G 843 MET cc_start: 0.5465 (mmm) cc_final: 0.5159 (mmm) REVERT: I 31 LYS cc_start: 0.8661 (ptpp) cc_final: 0.8201 (ptpp) REVERT: I 132 LYS cc_start: 0.8907 (mptt) cc_final: 0.8610 (mmmt) REVERT: I 175 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8658 (ptt-90) REVERT: I 548 VAL cc_start: 0.6551 (t) cc_final: 0.6323 (t) REVERT: I 645 ARG cc_start: 0.7702 (ttp-110) cc_final: 0.7475 (ttp-110) REVERT: I 712 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7109 (tp30) outliers start: 92 outliers final: 50 residues processed: 447 average time/residue: 0.2119 time to fit residues: 152.1065 Evaluate side-chains 394 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 339 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 555 HIS 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 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 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 577 LYS Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 230 SER 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 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 712 GLU 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: 0.5980 chunk 200 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 358 optimal weight: 0.4980 chunk 284 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 324 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 359 optimal weight: 7.9990 chunk 365 optimal weight: 0.7980 chunk 333 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 610 HIS G 354 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 = 0.3699 r_free = 0.3699 target = 0.097650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073138 restraints weight = 120098.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.075001 restraints weight = 63800.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.076217 restraints weight = 43451.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076978 restraints weight = 34083.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.077469 restraints weight = 29272.547| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1934 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= 0.119 Angle : 0.597 12.051 50201 Z= 0.299 Chirality : 0.043 0.160 5728 Planarity : 0.004 0.056 6278 Dihedral : 5.495 87.691 4937 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.50 % Allowed : 15.31 % Favored : 82.19 % 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: 0.70 (0.13), residues: 1734 sheet: -1.39 (0.25), residues: 460 loop : -1.54 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 119 TYR 0.026 0.001 TYR E 654 PHE 0.020 0.001 PHE A 781 TRP 0.016 0.001 TRP E 188 HIS 0.005 0.001 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (37140) covalent geometry : angle 0.59734 / 0.30 (50201) hydrogen bonds : bond 0.04103 / 2.70 ( 1262) hydrogen bonds : angle 4.37596 / 3.09 ( 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: 102 poor density : 373 time to evaluate : 1.452 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 157 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8161 (ptt90) REVERT: A 260 ASP cc_start: 0.7596 (p0) cc_final: 0.7262 (p0) REVERT: A 263 TYR cc_start: 0.8539 (m-80) cc_final: 0.7971 (m-80) REVERT: A 478 GLU cc_start: 0.7311 (tp30) cc_final: 0.7072 (tp30) REVERT: B 245 LYS cc_start: 0.6948 (mmpt) cc_final: 0.6610 (mmtt) REVERT: B 345 LYS cc_start: 0.8960 (pttp) cc_final: 0.8476 (mmtm) REVERT: C 27 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8213 (mmmt) REVERT: C 37 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.8982 (tp) REVERT: C 645 ARG cc_start: 0.7286 (ttp-170) cc_final: 0.7052 (ttp-170) REVERT: E 30 ARG cc_start: 0.8326 (mmt90) cc_final: 0.8123 (mtt90) REVERT: E 177 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8758 (tmmm) REVERT: E 690 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8178 (pp) REVERT: G 71 GLU cc_start: 0.8371 (tp30) cc_final: 0.7822 (tp30) REVERT: G 133 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7955 (mp10) REVERT: G 158 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8313 (tpt) REVERT: G 687 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8563 (tt) REVERT: I 27 LYS cc_start: 0.8547 (mmmt) cc_final: 0.8291 (mmmt) REVERT: I 31 LYS cc_start: 0.8553 (ptpp) cc_final: 0.8295 (ptpp) REVERT: I 44 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8159 (mp10) REVERT: I 132 LYS cc_start: 0.8930 (mptt) cc_final: 0.8679 (mmmt) REVERT: I 548 VAL cc_start: 0.6517 (t) cc_final: 0.6210 (t) outliers start: 102 outliers final: 62 residues processed: 449 average time/residue: 0.2178 time to fit residues: 156.4124 Evaluate side-chains 410 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 340 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 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 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 388 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 309 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 348 optimal weight: 0.9980 chunk 322 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 502 HIS E 610 HIS G 354 GLN I 517 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.095951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.071647 restraints weight = 119919.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.073462 restraints weight = 65328.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.074635 restraints weight = 44863.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.075363 restraints weight = 35424.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.075822 restraints weight = 30544.247| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 37140 Z= 0.194 Angle : 0.651 9.743 50201 Z= 0.330 Chirality : 0.045 0.173 5728 Planarity : 0.004 0.087 6278 Dihedral : 5.555 85.839 4930 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 3.33 % Allowed : 15.70 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.13), residues: 4488 helix: 0.61 (0.13), residues: 1767 sheet: -1.45 (0.25), residues: 460 loop : -1.62 (0.13), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 552 TYR 0.027 0.002 TYR E 654 PHE 0.018 0.002 PHE A 438 TRP 0.018 0.002 TRP I 285 HIS 0.007 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (37140) covalent geometry : angle 0.65130 / 0.33 (50201) hydrogen bonds : bond 0.04695 / 3.10 ( 1262) hydrogen bonds : angle 4.40623 / 3.11 ( 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 498 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 362 time to evaluate : 1.422 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: 0.7773 (p0) cc_final: 0.7446 (p0) REVERT: A 263 TYR cc_start: 0.8517 (m-80) cc_final: 0.8048 (m-80) REVERT: B 245 LYS cc_start: 0.6866 (mmpt) cc_final: 0.6525 (mmtt) REVERT: B 409 LYS cc_start: 0.8859 (mtmt) cc_final: 0.8635 (mtmt) REVERT: C 645 ARG cc_start: 0.7216 (ttp-170) cc_final: 0.7004 (ttp-170) REVERT: C 648 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7217 (mpp) REVERT: E 30 ARG cc_start: 0.8240 (mmt90) cc_final: 0.7943 (mmm-85) REVERT: E 177 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8806 (tmmm) REVERT: E 690 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8442 (pp) REVERT: G 71 GLU cc_start: 0.8405 (tp30) cc_final: 0.7920 (tp30) REVERT: G 133 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: G 158 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8263 (tpt) REVERT: G 687 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8617 (tt) REVERT: I 27 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8315 (mmmt) REVERT: I 31 LYS cc_start: 0.8615 (ptpp) cc_final: 0.8405 (ptpp) REVERT: I 44 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8213 (mp10) REVERT: I 548 VAL cc_start: 0.6532 (OUTLIER) cc_final: 0.6200 (t) outliers start: 136 outliers final: 86 residues processed: 470 average time/residue: 0.2150 time to fit residues: 162.7707 Evaluate side-chains 426 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 332 time to evaluate : 1.431 ------------------------------------------------------------------------------- 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 285 TRP 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 80 VAL 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 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 410 LEU 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 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 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 551 THR 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 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 770 LEU Chi-restraints excluded: chain I residue 44 GLN 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 440 GLU 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 639 TRP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 436 optimal weight: 5.9990 chunk 426 optimal weight: 0.9990 chunk 384 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 392 optimal weight: 3.9990 chunk 70 optimal weight: 0.0870 chunk 272 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 254 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 130 GLN C 407 ASN C 600 HIS ** E 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 354 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 = 0.3681 r_free = 0.3681 target = 0.096766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.072387 restraints weight = 120082.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.074229 restraints weight = 63764.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.075434 restraints weight = 43233.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.076193 restraints weight = 33854.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076660 restraints weight = 29111.473| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2286 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= 0.115 Angle : 0.608 11.754 50201 Z= 0.303 Chirality : 0.043 0.230 5728 Planarity : 0.004 0.085 6278 Dihedral : 5.333 89.187 4928 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 2.96 % Allowed : 16.65 % Favored : 80.38 % 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: 0.71 (0.13), residues: 1774 sheet: -1.43 (0.25), residues: 460 loop : -1.58 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 645 TYR 0.026 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/Z covalent geometry : bond 0.00259 / 0.12 (37140) covalent geometry : angle 0.60800 / 0.30 (50201) hydrogen bonds : bond 0.04047 / 2.67 ( 1262) hydrogen bonds : angle 4.24645 / 2.99 ( 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 483 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 362 time to evaluate : 1.425 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: 0.7671 (p0) cc_final: 0.7298 (p0) REVERT: A 263 TYR cc_start: 0.8463 (m-80) cc_final: 0.7960 (m-80) REVERT: A 478 GLU cc_start: 0.7195 (tp30) cc_final: 0.6892 (tp30) REVERT: A 854 ARG cc_start: 0.6474 (mmp-170) cc_final: 0.6265 (mmp-170) REVERT: B 245 LYS cc_start: 0.6861 (mmpt) cc_final: 0.6531 (mmtt) REVERT: B 345 LYS cc_start: 0.8962 (pttp) cc_final: 0.8436 (mmtm) REVERT: C 130 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7510 (mp10) REVERT: C 407 ASN cc_start: 0.6024 (m-40) cc_final: 0.5729 (m110) REVERT: C 648 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7173 (mpp) REVERT: C 797 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8086 (mm) REVERT: E 177 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8825 (tmmm) REVERT: E 690 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8400 (pp) REVERT: G 71 GLU cc_start: 0.8396 (tp30) cc_final: 0.7899 (tp30) REVERT: G 133 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: G 158 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8288 (tpt) REVERT: G 529 MET cc_start: 0.8024 (mmm) cc_final: 0.6276 (tpp) REVERT: G 549 ASP cc_start: 0.7924 (t70) cc_final: 0.7690 (t0) REVERT: G 687 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8594 (tt) REVERT: G 854 ARG cc_start: 0.3587 (tpt90) cc_final: 0.2038 (mmp80) REVERT: I 27 LYS cc_start: 0.8558 (mmmt) cc_final: 0.8296 (mmmt) REVERT: I 31 LYS cc_start: 0.8632 (ptpp) cc_final: 0.8400 (ptpp) REVERT: I 44 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8233 (mp10) REVERT: I 548 VAL cc_start: 0.6470 (OUTLIER) cc_final: 0.6128 (t) outliers start: 121 outliers final: 75 residues processed: 453 average time/residue: 0.2434 time to fit residues: 177.7804 Evaluate side-chains 421 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 336 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 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 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 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 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 137 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 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 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 770 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain G residue 34 GLU 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 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 649 CYS Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 44 GLN Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 126 GLU 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 548 VAL Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 670 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 52 optimal weight: 3.9990 chunk 226 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 320 optimal weight: 0.8980 chunk 345 optimal weight: 0.0670 chunk 308 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 364 optimal weight: 3.9990 chunk 427 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS C 44 GLN C 130 GLN E 610 HIS I 517 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.097054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.072651 restraints weight = 119883.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.074547 restraints weight = 64037.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.075776 restraints weight = 43265.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.076528 restraints weight = 33821.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.077015 restraints weight = 29079.971| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37140 Z= 0.123 Angle : 0.615 10.787 50201 Z= 0.306 Chirality : 0.043 0.199 5728 Planarity : 0.004 0.083 6278 Dihedral : 5.210 88.310 4924 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.91 % Allowed : 17.39 % Favored : 79.70 % 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: -0.92 (0.13), residues: 4488 helix: 0.77 (0.13), residues: 1774 sheet: -1.43 (0.25), residues: 460 loop : -1.58 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 119 TYR 0.027 0.001 TYR E 654 PHE 0.032 0.001 PHE E 683 TRP 0.011 0.001 TRP G 290 HIS 0.004 0.001 HIS E 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (37140) covalent geometry : angle 0.61487 / 0.31 (50201) hydrogen bonds : bond 0.03931 / 2.60 ( 1262) hydrogen bonds : angle 4.18398 / 2.94 ( 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 469 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 350 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.7683 (p0) cc_final: 0.7323 (p0) REVERT: A 263 TYR cc_start: 0.8505 (m-80) cc_final: 0.8099 (m-80) REVERT: A 478 GLU cc_start: 0.7287 (tp30) cc_final: 0.6965 (tp30) REVERT: A 873 MET cc_start: 0.3056 (ppp) cc_final: 0.2441 (tmm) REVERT: B 245 LYS cc_start: 0.6847 (mmpt) cc_final: 0.6601 (mmtt) REVERT: B 345 LYS cc_start: 0.8955 (pttp) cc_final: 0.8446 (mmtm) REVERT: C 126 GLU cc_start: 0.7765 (tp30) cc_final: 0.7497 (tp30) REVERT: C 407 ASN cc_start: 0.5963 (m-40) cc_final: 0.5604 (m110) REVERT: C 648 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7192 (mpp) REVERT: C 770 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8930 (pp) REVERT: C 797 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8221 (mm) REVERT: E 177 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8790 (tmmm) REVERT: E 552 ARG cc_start: 0.7327 (mmm160) cc_final: 0.7102 (mmm160) REVERT: E 690 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8368 (pp) REVERT: G 71 GLU cc_start: 0.8487 (tp30) cc_final: 0.8021 (tp30) REVERT: G 158 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8293 (tpt) REVERT: G 529 MET cc_start: 0.7721 (mmm) cc_final: 0.6424 (tpp) REVERT: G 549 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7671 (t0) REVERT: G 687 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8581 (tt) REVERT: G 854 ARG cc_start: 0.3606 (tpt90) cc_final: 0.2007 (mmp80) REVERT: I 27 LYS cc_start: 0.8584 (mmmt) cc_final: 0.8299 (mmmt) REVERT: I 31 LYS cc_start: 0.8642 (ptpp) cc_final: 0.8417 (ptpp) REVERT: I 548 VAL cc_start: 0.6500 (OUTLIER) cc_final: 0.6173 (t) outliers start: 119 outliers final: 88 residues processed: 441 average time/residue: 0.2304 time to fit residues: 163.9175 Evaluate side-chains 433 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 336 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLN 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 405 ASP Chi-restraints excluded: chain B residue 456 TYR 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 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 C residue 797 LEU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 137 LEU 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 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 656 MET Chi-restraints excluded: chain E residue 690 LEU 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 158 MET 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 549 ASP Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 598 LEU Chi-restraints excluded: chain G residue 687 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 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 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 Chi-restraints excluded: chain I residue 707 MET Chi-restraints excluded: chain I residue 715 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 137 optimal weight: 4.9990 chunk 269 optimal weight: 0.9980 chunk 309 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 439 optimal weight: 4.9990 chunk 202 optimal weight: 0.0170 chunk 271 optimal weight: 3.9990 chunk 397 optimal weight: 0.4980 chunk 342 optimal weight: 1.9990 chunk 416 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 432 HIS E 610 HIS G 130 GLN I 517 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.097068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073116 restraints weight = 119629.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.074951 restraints weight = 64754.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.076136 restraints weight = 44133.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.076865 restraints weight = 34742.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.077321 restraints weight = 29905.972| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37140 Z= 0.144 Angle : 0.628 10.682 50201 Z= 0.314 Chirality : 0.044 0.201 5728 Planarity : 0.004 0.068 6278 Dihedral : 5.220 88.792 4924 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.77 % Allowed : 17.98 % Favored : 79.26 % 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: -0.93 (0.13), residues: 4488 helix: 0.78 (0.13), residues: 1774 sheet: -1.50 (0.25), residues: 460 loop : -1.60 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 552 TYR 0.026 0.001 TYR E 654 PHE 0.027 0.001 PHE E 683 TRP 0.017 0.001 TRP E 188 HIS 0.004 0.001 HIS E 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (37140) covalent geometry : angle 0.62807 / 0.31 (50201) hydrogen bonds : bond 0.04060 / 2.68 ( 1262) hydrogen bonds : angle 4.17542 / 2.93 ( 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: 113 poor density : 355 time to evaluate : 1.412 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 31 LYS cc_start: 0.8640 (ttpp) cc_final: 0.8208 (tptp) REVERT: A 260 ASP cc_start: 0.7625 (p0) cc_final: 0.7256 (p0) REVERT: A 263 TYR cc_start: 0.8414 (m-80) cc_final: 0.8141 (m-80) REVERT: A 873 MET cc_start: 0.2164 (ppp) cc_final: 0.1645 (tmm) REVERT: B 245 LYS cc_start: 0.6835 (mmpt) cc_final: 0.6583 (mmtt) REVERT: C 31 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8273 (mmtm) REVERT: C 407 ASN cc_start: 0.5806 (m-40) cc_final: 0.5554 (m-40) REVERT: C 648 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7230 (mpp) REVERT: C 770 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8981 (pp) REVERT: E 177 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8741 (tmmm) REVERT: E 552 ARG cc_start: 0.7140 (mmm160) cc_final: 0.6900 (mmm160) REVERT: E 690 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8495 (pp) REVERT: G 71 GLU cc_start: 0.8320 (tp30) cc_final: 0.7969 (tp30) REVERT: G 158 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8213 (tpt) REVERT: G 549 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7442 (t0) REVERT: G 687 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8570 (tt) REVERT: G 854 ARG cc_start: 0.3630 (tpt90) cc_final: 0.2070 (mmp80) REVERT: I 27 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8175 (mmmt) REVERT: I 548 VAL cc_start: 0.6424 (OUTLIER) cc_final: 0.6081 (t) outliers start: 113 outliers final: 86 residues processed: 439 average time/residue: 0.2062 time to fit residues: 147.1687 Evaluate side-chains 431 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 337 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 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 375 MET 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 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 137 LEU 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 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 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 130 GLN Chi-restraints excluded: chain G residue 158 MET 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 479 LEU Chi-restraints excluded: chain G residue 549 ASP 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 284 optimal weight: 10.0000 chunk 358 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 205 optimal weight: 0.9980 chunk 404 optimal weight: 0.0010 chunk 147 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 417 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 407 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN B 432 HIS C 44 GLN E 610 HIS I 133 GLN I 517 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.097292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.073212 restraints weight = 119488.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.075087 restraints weight = 63929.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.076284 restraints weight = 43120.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.077048 restraints weight = 33785.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077447 restraints weight = 28919.796| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37140 Z= 0.118 Angle : 0.629 14.523 50201 Z= 0.311 Chirality : 0.043 0.189 5728 Planarity : 0.004 0.083 6278 Dihedral : 5.140 87.338 4924 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.62 % Allowed : 18.25 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 4488 helix: 0.82 (0.13), residues: 1769 sheet: -1.52 (0.25), residues: 460 loop : -1.60 (0.13), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 552 TYR 0.027 0.001 TYR E 654 PHE 0.025 0.001 PHE E 683 TRP 0.018 0.001 TRP E 188 HIS 0.008 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (37140) covalent geometry : angle 0.62947 / 0.31 (50201) hydrogen bonds : bond 0.03781 / 2.50 ( 1262) hydrogen bonds : angle 4.11354 / 2.89 ( 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 467 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 360 time to evaluate : 1.515 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: 0.7644 (p0) cc_final: 0.7250 (p0) REVERT: A 263 TYR cc_start: 0.8482 (m-80) cc_final: 0.8082 (m-80) REVERT: A 478 GLU cc_start: 0.7101 (tp30) cc_final: 0.6879 (tp30) REVERT: A 873 MET cc_start: 0.2335 (ppp) cc_final: 0.1823 (tmm) REVERT: B 245 LYS cc_start: 0.6802 (mmpt) cc_final: 0.6577 (mmtt) REVERT: B 345 LYS cc_start: 0.8950 (pttp) cc_final: 0.8377 (mmtm) REVERT: B 513 GLU cc_start: 0.5543 (pt0) cc_final: 0.5034 (tm-30) REVERT: C 31 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8299 (mmtm) REVERT: C 407 ASN cc_start: 0.5755 (m-40) cc_final: 0.5462 (m-40) REVERT: C 648 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7223 (mpp) REVERT: C 770 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8967 (pp) REVERT: C 843 MET cc_start: 0.7171 (mmm) cc_final: 0.6933 (mmm) REVERT: E 177 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8827 (tmmm) REVERT: E 552 ARG cc_start: 0.7306 (mmm160) cc_final: 0.7037 (mmm160) REVERT: E 690 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8415 (pp) REVERT: G 71 GLU cc_start: 0.8425 (tp30) cc_final: 0.8030 (tp30) REVERT: G 133 GLN cc_start: 0.8591 (mp10) cc_final: 0.7958 (mp10) REVERT: G 158 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8288 (tpt) REVERT: G 529 MET cc_start: 0.7994 (mmm) cc_final: 0.6427 (tpp) REVERT: G 549 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7614 (t0) REVERT: G 687 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8583 (tt) REVERT: G 854 ARG cc_start: 0.3601 (tpt90) cc_final: 0.2058 (mmp80) REVERT: G 873 MET cc_start: 0.4175 (tmm) cc_final: 0.3560 (tmm) REVERT: I 27 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8392 (mmmt) REVERT: I 31 LYS cc_start: 0.8658 (ptpp) cc_final: 0.8181 (ptpp) REVERT: I 548 VAL cc_start: 0.6484 (OUTLIER) cc_final: 0.6151 (t) outliers start: 107 outliers final: 88 residues processed: 442 average time/residue: 0.2300 time to fit residues: 164.4682 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 : 1.447 ------------------------------------------------------------------------------- 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 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 326 MET 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 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 410 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 26 GLU 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 137 LEU 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 484 MET 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 649 CYS Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 690 LEU 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 158 MET 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 549 ASP 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 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 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 591 ASP 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: 10.0000 chunk 259 optimal weight: 5.9990 chunk 319 optimal weight: 0.0040 chunk 2 optimal weight: 0.7980 chunk 448 optimal weight: 0.9980 chunk 431 optimal weight: 4.9990 chunk 400 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 0.0020 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 44 GLN E 610 HIS G 130 GLN G 354 GLN G 531 ASN I 133 GLN I 517 ASN I 531 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.097755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.073680 restraints weight = 119811.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.075601 restraints weight = 62970.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076830 restraints weight = 42109.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.077617 restraints weight = 32655.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.078107 restraints weight = 27809.067| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2716 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= 0.111 Angle : 0.636 13.664 50201 Z= 0.312 Chirality : 0.043 0.199 5728 Planarity : 0.004 0.100 6278 Dihedral : 5.047 84.632 4923 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.33 % Allowed : 18.88 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.13), residues: 4488 helix: 0.86 (0.13), residues: 1768 sheet: -1.53 (0.24), residues: 460 loop : -1.58 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG C 552 TYR 0.026 0.001 TYR E 654 PHE 0.025 0.001 PHE E 683 TRP 0.018 0.001 TRP E 188 HIS 0.003 0.000 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (37140) covalent geometry : angle 0.63583 / 0.31 (50201) hydrogen bonds : bond 0.03578 / 2.37 ( 1262) hydrogen bonds : angle 4.05374 / 2.85 ( 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 472 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 377 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.7624 (p0) cc_final: 0.7238 (p0) REVERT: A 263 TYR cc_start: 0.8460 (m-80) cc_final: 0.8118 (m-80) REVERT: A 478 GLU cc_start: 0.7062 (tp30) cc_final: 0.6826 (tp30) REVERT: A 873 MET cc_start: 0.2326 (ppp) cc_final: 0.1797 (tmm) REVERT: B 245 LYS cc_start: 0.6735 (mmpt) cc_final: 0.6508 (mmtt) REVERT: B 274 TYR cc_start: 0.6887 (t80) cc_final: 0.6652 (t80) REVERT: B 345 LYS cc_start: 0.8937 (pttp) cc_final: 0.8347 (mmtm) REVERT: B 513 GLU cc_start: 0.5522 (pt0) cc_final: 0.4937 (tm-30) REVERT: C 407 ASN cc_start: 0.5606 (m-40) cc_final: 0.5347 (m-40) REVERT: C 648 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7211 (mpp) REVERT: C 770 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8966 (pp) REVERT: E 119 ARG cc_start: 0.7407 (ptp90) cc_final: 0.7071 (ptt-90) REVERT: E 177 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8843 (tmmm) REVERT: E 552 ARG cc_start: 0.7327 (mmm160) cc_final: 0.7027 (mmm160) REVERT: E 690 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8324 (pp) REVERT: G 71 GLU cc_start: 0.8404 (tp30) cc_final: 0.8003 (tp30) REVERT: G 133 GLN cc_start: 0.8499 (mp10) cc_final: 0.7889 (mp10) REVERT: G 158 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8279 (tpt) REVERT: G 529 MET cc_start: 0.8015 (mmm) cc_final: 0.6601 (tpp) REVERT: G 549 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7579 (t0) REVERT: G 687 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8552 (tt) REVERT: G 854 ARG cc_start: 0.3547 (tpt90) cc_final: 0.2010 (mmp80) REVERT: I 31 LYS cc_start: 0.8619 (ptpp) cc_final: 0.8150 (ptpp) REVERT: I 548 VAL cc_start: 0.6536 (OUTLIER) cc_final: 0.6215 (t) REVERT: I 637 LEU cc_start: 0.9036 (mm) cc_final: 0.8812 (mt) outliers start: 95 outliers final: 83 residues processed: 450 average time/residue: 0.2396 time to fit residues: 173.6224 Evaluate side-chains 445 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 354 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 625 LEU 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 80 VAL 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 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 410 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 44 GLN Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 137 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 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 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 636 VAL Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 690 LEU 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 130 GLN Chi-restraints excluded: chain G residue 158 MET 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 466 ILE Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 549 ASP 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 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 Chi-restraints excluded: chain I residue 856 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.776 > 50: distance: 67 - 71: 8.380 distance: 71 - 72: 26.659 distance: 72 - 73: 15.355 distance: 73 - 74: 59.776 distance: 73 - 75: 45.629 distance: 75 - 76: 17.677 distance: 76 - 77: 23.040 distance: 76 - 79: 16.115 distance: 77 - 78: 7.133 distance: 77 - 82: 16.454 distance: 79 - 80: 20.126 distance: 79 - 81: 9.231 distance: 82 - 83: 23.833 distance: 83 - 84: 18.448 distance: 83 - 86: 36.023 distance: 84 - 85: 19.282 distance: 84 - 91: 5.957 distance: 86 - 87: 21.845 distance: 87 - 88: 18.682 distance: 88 - 89: 14.581 distance: 89 - 90: 10.148 distance: 91 - 92: 21.307 distance: 92 - 93: 31.661 distance: 92 - 95: 10.231 distance: 93 - 94: 25.125 distance: 93 - 99: 26.210 distance: 95 - 96: 8.241 distance: 95 - 97: 8.912 distance: 96 - 98: 13.944 distance: 99 - 100: 7.276 distance: 100 - 101: 16.473 distance: 101 - 102: 26.143 distance: 101 - 108: 19.566 distance: 103 - 104: 12.726 distance: 104 - 105: 6.595 distance: 105 - 106: 13.796 distance: 105 - 107: 10.741 distance: 108 - 109: 11.985 distance: 109 - 110: 30.398 distance: 109 - 112: 12.908 distance: 110 - 111: 27.621 distance: 110 - 115: 17.508 distance: 112 - 113: 7.923 distance: 112 - 114: 8.007 distance: 115 - 116: 14.444 distance: 116 - 117: 36.243 distance: 116 - 119: 37.239 distance: 117 - 118: 38.935 distance: 117 - 123: 16.990 distance: 119 - 120: 34.946 distance: 120 - 121: 23.779 distance: 120 - 122: 32.322 distance: 123 - 124: 11.465 distance: 123 - 129: 7.191 distance: 124 - 125: 7.405 distance: 124 - 127: 15.620 distance: 125 - 126: 7.953 distance: 125 - 130: 29.027 distance: 127 - 128: 26.859 distance: 128 - 129: 28.300 distance: 130 - 131: 15.801 distance: 131 - 132: 14.377 distance: 131 - 134: 4.164 distance: 132 - 133: 10.226 distance: 132 - 144: 10.534 distance: 134 - 135: 8.525 distance: 135 - 136: 7.635 distance: 136 - 138: 9.049 distance: 137 - 139: 6.861 distance: 137 - 140: 6.516 distance: 138 - 139: 5.031 distance: 139 - 141: 3.479 distance: 140 - 142: 4.275 distance: 141 - 143: 5.149 distance: 142 - 143: 5.328 distance: 144 - 145: 10.032 distance: 145 - 146: 15.090 distance: 145 - 148: 10.678 distance: 146 - 147: 7.426 distance: 146 - 150: 13.000 distance: 148 - 149: 5.061