Starting phenix.real_space_refine on Tue Aug 26 11:19:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9exq_50046/08_2025/9exq_50046.cif Found real_map, /net/cci-nas-00/data/ceres_data/9exq_50046/08_2025/9exq_50046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9exq_50046/08_2025/9exq_50046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9exq_50046/08_2025/9exq_50046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9exq_50046/08_2025/9exq_50046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9exq_50046/08_2025/9exq_50046.map" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 113 5.16 5 C 23349 2.51 5 N 6261 2.21 5 O 6956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36703 Number of models: 1 Model: "" Number of chains: 16 Chain: "D" Number of atoms: 5103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5103 Classifications: {'peptide': 656} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 630} Chain breaks: 3 Chain: "E" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3966 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 492} Chain breaks: 3 Chain: "F" Number of atoms: 5103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5103 Classifications: {'peptide': 656} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 630} Chain breaks: 3 Chain: "G" Number of atoms: 4299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4299 Classifications: {'peptide': 557} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 533} Chain breaks: 3 Chain: "H" Number of atoms: 4303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4303 Classifications: {'peptide': 558} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 534} Chain breaks: 3 Chain: "A" Number of atoms: 5103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5103 Classifications: {'peptide': 656} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 630} Chain breaks: 3 Chain: "B" Number of atoms: 4299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4299 Classifications: {'peptide': 557} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 533} Chain breaks: 3 Chain: "C" Number of atoms: 4303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4303 Classifications: {'peptide': 558} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 534} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.82, per 1000 atoms: 0.24 Number of scatterers: 36703 At special positions: 0 Unit cell: (163.614, 165.088, 175.406, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 113 16.00 P 16 15.00 Mg 8 11.99 O 6956 8.00 N 6261 7.00 C 23349 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: 3.65 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8762 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 32 sheets defined 50.8% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 29 through 51 Processing helix chain 'D' and resid 86 through 94 removed outlier: 3.540A pdb=" N THR D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 208 through 219 removed outlier: 3.682A pdb=" N SER D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 260 removed outlier: 4.087A pdb=" N SER D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 266 removed outlier: 3.781A pdb=" N GLN D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 297 Proline residue: D 279 - end of helix Processing helix chain 'D' and resid 305 through 336 removed outlier: 3.681A pdb=" N GLN D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 335 " --> pdb=" O GLU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 366 removed outlier: 3.531A pdb=" N LEU D 346 " --> pdb=" O THR D 342 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET D 347 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU D 348 " --> pdb=" O LYS D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 404 removed outlier: 3.861A pdb=" N VAL D 374 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER D 403 " --> pdb=" O ASN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 451 Processing helix chain 'D' and resid 457 through 465 removed outlier: 4.132A pdb=" N LEU D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 504 through 521 removed outlier: 3.690A pdb=" N PHE D 519 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 553 Processing helix chain 'D' and resid 569 through 575 Processing helix chain 'D' and resid 581 through 587 removed outlier: 3.572A pdb=" N PHE D 585 " --> pdb=" O GLY D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 620 Processing helix chain 'D' and resid 622 through 633 removed outlier: 4.293A pdb=" N GLU D 626 " --> pdb=" O HIS D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 Processing helix chain 'D' and resid 657 through 659 No H-bonds generated for 'chain 'D' and resid 657 through 659' Processing helix chain 'D' and resid 672 through 686 removed outlier: 3.578A pdb=" N SER D 686 " --> pdb=" O ARG D 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 29 through 51 Processing helix chain 'E' and resid 86 through 94 removed outlier: 3.709A pdb=" N THR E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 107 Processing helix chain 'E' and resid 120 through 128 Processing helix chain 'E' and resid 208 through 219 removed outlier: 3.562A pdb=" N SER E 219 " --> pdb=" O ASP E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 260 removed outlier: 4.019A pdb=" N SER E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 451 Processing helix chain 'E' and resid 457 through 465 removed outlier: 4.097A pdb=" N LEU E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE E 464 " --> pdb=" O GLN E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 501 Processing helix chain 'E' and resid 504 through 521 removed outlier: 3.664A pdb=" N PHE E 519 " --> pdb=" O THR E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 553 Processing helix chain 'E' and resid 569 through 575 Processing helix chain 'E' and resid 581 through 587 removed outlier: 3.687A pdb=" N PHE E 585 " --> pdb=" O GLY E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 620 Processing helix chain 'E' and resid 622 through 633 removed outlier: 4.267A pdb=" N GLU E 626 " --> pdb=" O HIS E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 656 Processing helix chain 'E' and resid 657 through 659 No H-bonds generated for 'chain 'E' and resid 657 through 659' Processing helix chain 'E' and resid 672 through 686 removed outlier: 3.537A pdb=" N SER E 686 " --> pdb=" O ARG E 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 removed outlier: 3.502A pdb=" N VAL F 22 " --> pdb=" O ASP F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 51 Processing helix chain 'F' and resid 86 through 94 removed outlier: 3.671A pdb=" N GLN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 107 Processing helix chain 'F' and resid 120 through 128 Processing helix chain 'F' and resid 208 through 219 removed outlier: 3.609A pdb=" N SER F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 266 removed outlier: 3.691A pdb=" N ARG F 262 " --> pdb=" O GLN F 258 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN F 263 " --> pdb=" O ASN F 259 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA F 264 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN F 266 " --> pdb=" O ARG F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 297 Proline residue: F 279 - end of helix Processing helix chain 'F' and resid 305 through 336 Processing helix chain 'F' and resid 340 through 367 removed outlier: 3.711A pdb=" N MET F 347 " --> pdb=" O TYR F 343 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 403 removed outlier: 4.198A pdb=" N VAL F 374 " --> pdb=" O THR F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 451 Processing helix chain 'F' and resid 457 through 465 removed outlier: 4.138A pdb=" N LEU F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 504 through 521 removed outlier: 3.683A pdb=" N PHE F 519 " --> pdb=" O THR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 553 Processing helix chain 'F' and resid 569 through 575 Processing helix chain 'F' and resid 581 through 587 removed outlier: 3.686A pdb=" N PHE F 585 " --> pdb=" O GLY F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 620 Processing helix chain 'F' and resid 622 through 633 removed outlier: 4.287A pdb=" N GLU F 626 " --> pdb=" O HIS F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 656 Processing helix chain 'F' and resid 657 through 659 No H-bonds generated for 'chain 'F' and resid 657 through 659' Processing helix chain 'F' and resid 672 through 686 Processing helix chain 'G' and resid 18 through 29 removed outlier: 3.603A pdb=" N VAL G 22 " --> pdb=" O ASP G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 51 Processing helix chain 'G' and resid 86 through 94 removed outlier: 3.855A pdb=" N THR G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 208 through 219 removed outlier: 3.665A pdb=" N SER G 219 " --> pdb=" O ASP G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 277 Processing helix chain 'G' and resid 386 through 404 Processing helix chain 'G' and resid 425 through 451 Processing helix chain 'G' and resid 457 through 465 removed outlier: 4.064A pdb=" N LEU G 461 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE G 464 " --> pdb=" O GLN G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 501 Processing helix chain 'G' and resid 504 through 521 removed outlier: 3.669A pdb=" N PHE G 519 " --> pdb=" O THR G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 553 Processing helix chain 'G' and resid 569 through 575 Processing helix chain 'G' and resid 581 through 587 removed outlier: 3.619A pdb=" N PHE G 585 " --> pdb=" O GLY G 581 " (cutoff:3.500A) Processing helix chain 'G' and resid 615 through 620 Processing helix chain 'G' and resid 622 through 633 removed outlier: 4.258A pdb=" N GLU G 626 " --> pdb=" O HIS G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 656 Processing helix chain 'G' and resid 657 through 659 No H-bonds generated for 'chain 'G' and resid 657 through 659' Processing helix chain 'G' and resid 672 through 686 removed outlier: 3.500A pdb=" N SER G 686 " --> pdb=" O ARG G 682 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 removed outlier: 3.537A pdb=" N VAL H 22 " --> pdb=" O ASP H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 51 Processing helix chain 'H' and resid 86 through 94 removed outlier: 4.071A pdb=" N THR H 90 " --> pdb=" O SER H 86 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'H' and resid 120 through 128 Processing helix chain 'H' and resid 208 through 219 removed outlier: 3.662A pdb=" N SER H 219 " --> pdb=" O ASP H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 264 removed outlier: 3.956A pdb=" N SER H 245 " --> pdb=" O PRO H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 278 Processing helix chain 'H' and resid 385 through 404 Processing helix chain 'H' and resid 425 through 451 Processing helix chain 'H' and resid 457 through 465 removed outlier: 4.081A pdb=" N LEU H 461 " --> pdb=" O SER H 457 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE H 464 " --> pdb=" O GLN H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 501 Processing helix chain 'H' and resid 504 through 521 removed outlier: 3.716A pdb=" N PHE H 519 " --> pdb=" O THR H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 553 Processing helix chain 'H' and resid 569 through 575 Processing helix chain 'H' and resid 581 through 587 removed outlier: 3.565A pdb=" N PHE H 585 " --> pdb=" O GLY H 581 " (cutoff:3.500A) Processing helix chain 'H' and resid 615 through 620 Processing helix chain 'H' and resid 622 through 633 removed outlier: 4.268A pdb=" N GLU H 626 " --> pdb=" O HIS H 622 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 656 Processing helix chain 'H' and resid 657 through 659 No H-bonds generated for 'chain 'H' and resid 657 through 659' Processing helix chain 'H' and resid 672 through 686 removed outlier: 3.510A pdb=" N SER H 686 " --> pdb=" O ARG H 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 29 removed outlier: 3.508A pdb=" N VAL A 22 " --> pdb=" O ASP A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 51 Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.712A pdb=" N GLN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 107 removed outlier: 3.548A pdb=" N LEU A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.716A pdb=" N SER A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 263 removed outlier: 3.935A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN A 263 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 297 removed outlier: 3.734A pdb=" N GLN A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 305 through 336 removed outlier: 3.609A pdb=" N GLN A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 367 removed outlier: 3.768A pdb=" N SER A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 404 removed outlier: 3.644A pdb=" N GLN A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 397 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 451 Processing helix chain 'A' and resid 457 through 465 removed outlier: 4.079A pdb=" N LEU A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 504 through 521 removed outlier: 3.625A pdb=" N PHE A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 569 through 575 Processing helix chain 'A' and resid 581 through 587 removed outlier: 3.736A pdb=" N PHE A 585 " --> pdb=" O GLY A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 621 removed outlier: 3.702A pdb=" N MET A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 633 removed outlier: 4.276A pdb=" N GLU A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 672 through 686 removed outlier: 3.558A pdb=" N SER A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.869A pdb=" N VAL B 22 " --> pdb=" O ASP B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.834A pdb=" N THR B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 208 through 219 removed outlier: 3.569A pdb=" N SER B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 278 removed outlier: 3.933A pdb=" N SER B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG B 262 " --> pdb=" O GLN B 258 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 425 through 451 Processing helix chain 'B' and resid 457 through 465 removed outlier: 4.155A pdb=" N LEU B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 504 through 521 removed outlier: 3.687A pdb=" N PHE B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 553 Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 581 through 587 removed outlier: 3.703A pdb=" N PHE B 585 " --> pdb=" O GLY B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 621 removed outlier: 3.718A pdb=" N MET B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 633 removed outlier: 4.266A pdb=" N GLU B 626 " --> pdb=" O HIS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 656 Processing helix chain 'B' and resid 657 through 659 No H-bonds generated for 'chain 'B' and resid 657 through 659' Processing helix chain 'B' and resid 672 through 686 removed outlier: 3.595A pdb=" N SER B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 29 through 51 Processing helix chain 'C' and resid 86 through 94 removed outlier: 3.999A pdb=" N THR C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 208 through 219 removed outlier: 3.661A pdb=" N SER C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 264 removed outlier: 4.077A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 385 through 405 Processing helix chain 'C' and resid 425 through 451 Processing helix chain 'C' and resid 457 through 465 removed outlier: 4.085A pdb=" N LEU C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 504 through 521 removed outlier: 3.657A pdb=" N PHE C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 553 Processing helix chain 'C' and resid 569 through 575 Processing helix chain 'C' and resid 581 through 587 removed outlier: 3.635A pdb=" N PHE C 585 " --> pdb=" O GLY C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 620 Processing helix chain 'C' and resid 622 through 633 removed outlier: 4.227A pdb=" N GLU C 626 " --> pdb=" O HIS C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 657 through 659 No H-bonds generated for 'chain 'C' and resid 657 through 659' Processing helix chain 'C' and resid 672 through 686 removed outlier: 3.542A pdb=" N SER C 686 " --> pdb=" O ARG C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 705 removed outlier: 3.893A pdb=" N TYR C 705 " --> pdb=" O ALA C 702 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 220 through 223 removed outlier: 8.499A pdb=" N ILE D 54 " --> pdb=" O ASP D 418 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ASP D 418 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU D 56 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL D 416 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP D 58 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASN D 414 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU D 60 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 110 through 114 Processing sheet with id=AA3, first strand: chain 'D' and resid 134 through 141 removed outlier: 7.415A pdb=" N ASN D 134 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE D 194 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU D 190 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU D 140 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER D 188 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 468 through 473 removed outlier: 8.434A pdb=" N VAL D 468 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N ASN D 696 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 10.582A pdb=" N ALA D 470 " --> pdb=" O ASN D 696 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N VAL D 698 " --> pdb=" O ALA D 470 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE D 472 " --> pdb=" O VAL D 698 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N CYS D 662 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ILE D 694 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU D 664 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASN D 696 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA D 666 " --> pdb=" O ASN D 696 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL D 698 " --> pdb=" O ALA D 666 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 220 through 223 removed outlier: 6.858A pdb=" N GLU E 56 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL E 416 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP E 58 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASN E 414 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU E 60 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 110 through 114 Processing sheet with id=AA7, first strand: chain 'E' and resid 134 through 141 removed outlier: 7.150A pdb=" N ASN E 134 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE E 194 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR E 138 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU E 190 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU E 140 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER E 188 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 468 through 473 removed outlier: 7.422A pdb=" N LEU E 695 " --> pdb=" O TYR E 469 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER E 471 " --> pdb=" O LEU E 695 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY E 697 " --> pdb=" O SER E 471 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N CYS E 662 " --> pdb=" O GLY E 692 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ILE E 694 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU E 664 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASN E 696 " --> pdb=" O LEU E 664 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA E 666 " --> pdb=" O ASN E 696 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL E 698 " --> pdb=" O ALA E 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 220 through 223 removed outlier: 8.652A pdb=" N ILE F 54 " --> pdb=" O ASP F 418 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ASP F 418 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLU F 56 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL F 416 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP F 58 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASN F 414 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU F 60 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 110 through 114 Processing sheet with id=AB2, first strand: chain 'F' and resid 134 through 141 removed outlier: 7.316A pdb=" N ASN F 134 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE F 194 " --> pdb=" O ASN F 134 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU F 190 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU F 140 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER F 188 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 468 through 473 removed outlier: 7.403A pdb=" N LEU F 695 " --> pdb=" O TYR F 469 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER F 471 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLY F 697 " --> pdb=" O SER F 471 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY F 692 " --> pdb=" O CYS F 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 220 through 223 removed outlier: 8.606A pdb=" N ILE G 54 " --> pdb=" O ASP G 418 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASP G 418 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU G 56 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL G 416 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP G 58 " --> pdb=" O ASN G 414 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASN G 414 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU G 60 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 110 through 114 Processing sheet with id=AB6, first strand: chain 'G' and resid 134 through 141 removed outlier: 7.251A pdb=" N ASN G 134 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ILE G 194 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU G 190 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU G 140 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER G 188 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 468 through 473 removed outlier: 7.362A pdb=" N LEU G 695 " --> pdb=" O TYR G 469 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER G 471 " --> pdb=" O LEU G 695 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY G 697 " --> pdb=" O SER G 471 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N CYS G 662 " --> pdb=" O GLY G 692 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ILE G 694 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU G 664 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASN G 696 " --> pdb=" O LEU G 664 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA G 666 " --> pdb=" O ASN G 696 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL G 698 " --> pdb=" O ALA G 666 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 220 through 223 removed outlier: 8.633A pdb=" N ILE H 54 " --> pdb=" O ASP H 418 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ASP H 418 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU H 56 " --> pdb=" O VAL H 416 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL H 416 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP H 58 " --> pdb=" O ASN H 414 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASN H 414 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU H 60 " --> pdb=" O ILE H 412 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 110 through 114 Processing sheet with id=AC1, first strand: chain 'H' and resid 134 through 141 removed outlier: 7.298A pdb=" N ILE H 135 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE H 194 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE H 137 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN H 192 " --> pdb=" O ILE H 137 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG H 139 " --> pdb=" O LEU H 190 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 468 through 473 removed outlier: 7.447A pdb=" N LEU H 695 " --> pdb=" O TYR H 469 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER H 471 " --> pdb=" O LEU H 695 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY H 697 " --> pdb=" O SER H 471 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N CYS H 662 " --> pdb=" O GLY H 692 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ILE H 694 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU H 664 " --> pdb=" O ILE H 694 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASN H 696 " --> pdb=" O LEU H 664 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA H 666 " --> pdb=" O ASN H 696 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL H 698 " --> pdb=" O ALA H 666 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 220 through 223 removed outlier: 6.880A pdb=" N GLU A 56 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 416 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP A 58 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ASN A 414 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 60 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AC5, first strand: chain 'A' and resid 134 through 141 removed outlier: 7.242A pdb=" N ASN A 134 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE A 194 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU A 190 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU A 140 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER A 188 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 468 through 473 removed outlier: 7.428A pdb=" N LEU A 695 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 471 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLY A 697 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N CYS A 662 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE A 694 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 664 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASN A 696 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA A 666 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL A 698 " --> pdb=" O ALA A 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 220 through 223 removed outlier: 7.037A pdb=" N GLU B 56 " --> pdb=" O PRO B 421 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N ASP B 58 " --> pdb=" O PRO B 419 " (cutoff:3.500A) removed outlier: 12.672A pdb=" N LEU B 60 " --> pdb=" O THR B 417 " (cutoff:3.500A) removed outlier: 12.884A pdb=" N THR B 417 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 14.121A pdb=" N GLN B 62 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 13.648A pdb=" N ALA B 415 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AC9, first strand: chain 'B' and resid 134 through 141 removed outlier: 7.477A pdb=" N ASN B 134 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ILE B 194 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 138 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU B 190 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU B 140 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER B 188 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 468 through 473 removed outlier: 8.463A pdb=" N VAL B 468 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 10.406A pdb=" N ASN B 696 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N ALA B 470 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N VAL B 698 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE B 472 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N CYS B 662 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ILE B 694 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 664 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN B 696 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 666 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 698 " --> pdb=" O ALA B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 220 through 223 removed outlier: 8.572A pdb=" N ILE C 54 " --> pdb=" O ASP C 418 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ASP C 418 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU C 56 " --> pdb=" O VAL C 416 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL C 416 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASP C 58 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ASN C 414 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU C 60 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AD4, first strand: chain 'C' and resid 134 through 141 removed outlier: 7.199A pdb=" N ILE C 135 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE C 194 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE C 137 " --> pdb=" O ASN C 192 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASN C 192 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG C 139 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 468 through 473 removed outlier: 7.418A pdb=" N LEU C 695 " --> pdb=" O TYR C 469 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER C 471 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY C 697 " --> pdb=" O SER C 471 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N CYS C 662 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ILE C 694 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU C 664 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASN C 696 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA C 666 " --> pdb=" O ASN C 696 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL C 698 " --> pdb=" O ALA C 666 " (cutoff:3.500A) 2048 hydrogen bonds defined for protein. 6024 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: 8.53 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 11814 1.33 - 1.45: 4014 1.45 - 1.57: 21170 1.57 - 1.69: 41 1.69 - 1.80: 210 Bond restraints: 37249 Sorted by residual: bond pdb=" C3' ADP B1000 " pdb=" C4' ADP B1000 " ideal model delta sigma weight residual 1.524 1.269 0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" C3' ADP D1000 " pdb=" C4' ADP D1000 " ideal model delta sigma weight residual 1.524 1.269 0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" C3' ADP A1000 " pdb=" C4' ADP A1000 " ideal model delta sigma weight residual 1.524 1.269 0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" C3' ADP H1000 " pdb=" C4' ADP H1000 " ideal model delta sigma weight residual 1.524 1.269 0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" C3' ADP E1000 " pdb=" C4' ADP E1000 " ideal model delta sigma weight residual 1.524 1.269 0.255 2.00e-02 2.50e+03 1.62e+02 ... (remaining 37244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 50140 3.46 - 6.92: 256 6.92 - 10.38: 44 10.38 - 13.84: 36 13.84 - 17.30: 1 Bond angle restraints: 50477 Sorted by residual: angle pdb=" N PRO A 143 " pdb=" CD PRO A 143 " pdb=" CG PRO A 143 " ideal model delta sigma weight residual 103.20 85.90 17.30 1.50e+00 4.44e-01 1.33e+02 angle pdb=" CA PRO A 143 " pdb=" N PRO A 143 " pdb=" CD PRO A 143 " ideal model delta sigma weight residual 112.00 103.02 8.98 1.40e+00 5.10e-01 4.11e+01 angle pdb=" CA PRO A 143 " pdb=" CB PRO A 143 " pdb=" CG PRO A 143 " ideal model delta sigma weight residual 104.50 93.16 11.34 1.90e+00 2.77e-01 3.56e+01 angle pdb=" N VAL F 119 " pdb=" CA VAL F 119 " pdb=" C VAL F 119 " ideal model delta sigma weight residual 112.80 107.40 5.40 1.15e+00 7.56e-01 2.20e+01 angle pdb=" CB ARG E 410 " pdb=" CG ARG E 410 " pdb=" CD ARG E 410 " ideal model delta sigma weight residual 111.30 100.74 10.56 2.30e+00 1.89e-01 2.11e+01 ... (remaining 50472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.06: 22285 27.06 - 54.13: 395 54.13 - 81.19: 53 81.19 - 108.25: 6 108.25 - 135.32: 16 Dihedral angle restraints: 22755 sinusoidal: 9168 harmonic: 13587 Sorted by residual: dihedral pdb=" O1B ADP A1000 " pdb=" O3A ADP A1000 " pdb=" PB ADP A1000 " pdb=" PA ADP A1000 " ideal model delta sinusoidal sigma weight residual 300.00 164.68 135.32 1 2.00e+01 2.50e-03 4.11e+01 dihedral pdb=" CA GLY D 407 " pdb=" C GLY D 407 " pdb=" N ASN D 408 " pdb=" CA ASN D 408 " ideal model delta harmonic sigma weight residual 180.00 148.22 31.78 0 5.00e+00 4.00e-02 4.04e+01 dihedral pdb=" O1B ADP E1000 " pdb=" O3A ADP E1000 " pdb=" PB ADP E1000 " pdb=" PA ADP E1000 " ideal model delta sinusoidal sigma weight residual 300.00 169.07 130.93 1 2.00e+01 2.50e-03 3.97e+01 ... (remaining 22752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3683 0.037 - 0.074: 1521 0.074 - 0.111: 575 0.111 - 0.149: 204 0.149 - 0.186: 18 Chirality restraints: 6001 Sorted by residual: chirality pdb=" CA GLU C 193 " pdb=" N GLU C 193 " pdb=" C GLU C 193 " pdb=" CB GLU C 193 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" CA GLU A 684 " pdb=" N GLU A 684 " pdb=" C GLU A 684 " pdb=" CB GLU A 684 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA MET G 521 " pdb=" N MET G 521 " pdb=" C MET G 521 " pdb=" CB MET G 521 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.66e-01 ... (remaining 5998 not shown) Planarity restraints: 6425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 142 " -0.073 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO A 143 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 143 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 143 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 408 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C ASN D 408 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN D 408 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL D 409 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 708 " -0.003 2.00e-02 2.50e+03 1.32e-02 3.50e+00 pdb=" CG TYR F 708 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR F 708 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR F 708 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR F 708 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR F 708 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 708 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR F 708 " 0.001 2.00e-02 2.50e+03 ... (remaining 6422 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.46: 198 2.46 - 3.07: 27024 3.07 - 3.68: 54019 3.68 - 4.29: 79983 4.29 - 4.90: 133020 Nonbonded interactions: 294244 Sorted by model distance: nonbonded pdb=" O3B ADP C1000 " pdb="MG MG C1001 " model vdw 1.856 2.170 nonbonded pdb=" O3B ADP B1000 " pdb="MG MG B1001 " model vdw 1.869 2.170 nonbonded pdb=" O3B ADP A1000 " pdb="MG MG A1001 " model vdw 1.870 2.170 nonbonded pdb=" O3B ADP D1000 " pdb="MG MG D1001 " model vdw 1.876 2.170 nonbonded pdb=" O3B ADP E1000 " pdb="MG MG E1001 " model vdw 1.881 2.170 ... (remaining 294239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 279 or resid 384 through 1001)) selection = chain 'C' selection = (chain 'D' and (resid 17 through 279 or resid 384 through 1001)) selection = (chain 'F' and (resid 17 through 279 or resid 384 through 1001)) selection = chain 'H' } ncs_group { reference = (chain 'B' and (resid 17 through 261 or resid 409 through 1001)) selection = chain 'E' selection = (chain 'G' and (resid 17 through 261 or resid 409 through 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.610 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: 0.050 Extract box with map and model: 0.860 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 34.500 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 : 0.011 0.282 37249 Z= 0.484 Angle : 0.814 17.300 50477 Z= 0.409 Chirality : 0.049 0.186 6001 Planarity : 0.004 0.104 6425 Dihedral : 11.757 135.319 13993 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.69 (0.12), residues: 4649 helix: 1.61 (0.11), residues: 2222 sheet: 0.90 (0.18), residues: 768 loop : -1.40 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 667 TYR 0.026 0.002 TYR F 708 PHE 0.033 0.002 PHE D 40 TRP 0.015 0.002 TRP F 477 HIS 0.005 0.001 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.01054 (37249) covalent geometry : angle 0.81372 (50477) hydrogen bonds : bond 0.15461 ( 2048) hydrogen bonds : angle 5.91867 ( 6024) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 519 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 446 LEU cc_start: 0.8176 (tt) cc_final: 0.7794 (mp) REVERT: D 621 MET cc_start: 0.8648 (mtp) cc_final: 0.8446 (mtp) REVERT: D 657 ARG cc_start: 0.7329 (mtm-85) cc_final: 0.6993 (mtm-85) REVERT: D 707 ARG cc_start: 0.5791 (tpm170) cc_final: 0.5314 (mpt-90) REVERT: E 89 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7310 (mm-30) REVERT: F 89 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7671 (mm-30) REVERT: F 165 TYR cc_start: 0.8288 (p90) cc_final: 0.7949 (p90) REVERT: F 210 LEU cc_start: 0.7993 (tt) cc_final: 0.7249 (mm) REVERT: F 658 TYR cc_start: 0.8261 (m-80) cc_final: 0.8050 (m-80) REVERT: G 675 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7304 (mt-10) REVERT: H 122 ARG cc_start: 0.8325 (ttt180) cc_final: 0.8093 (ttt180) REVERT: B 101 LYS cc_start: 0.7762 (ttmt) cc_final: 0.7337 (tptm) REVERT: C 420 ASN cc_start: 0.7741 (m-40) cc_final: 0.7084 (p0) REVERT: C 540 MET cc_start: 0.8318 (mtm) cc_final: 0.8097 (mtt) REVERT: C 658 TYR cc_start: 0.8234 (m-80) cc_final: 0.7842 (m-80) outliers start: 0 outliers final: 2 residues processed: 519 average time/residue: 0.6926 time to fit residues: 434.8707 Evaluate side-chains 370 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 368 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain B residue 239 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 0.4980 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 173 GLN E 259 ASN E 589 GLN E 611 GLN E 635 ASN E 710 HIS F 266 GLN G 408 ASN G 611 GLN G 671 ASN H 206 GLN H 258 GLN H 710 HIS A 340 HIS A 518 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN C 399 ASN C 710 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.213217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124939 restraints weight = 38774.894| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.45 r_work: 0.3190 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 37249 Z= 0.119 Angle : 0.608 12.380 50477 Z= 0.299 Chirality : 0.044 0.182 6001 Planarity : 0.004 0.056 6425 Dihedral : 8.945 142.595 5127 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.29 % Allowed : 6.30 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 1.09 (0.12), residues: 4649 helix: 1.99 (0.11), residues: 2284 sheet: 1.21 (0.18), residues: 746 loop : -1.44 (0.14), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 410 TYR 0.019 0.001 TYR A 141 PHE 0.021 0.002 PHE G 447 TRP 0.006 0.001 TRP F 477 HIS 0.013 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00256 (37249) covalent geometry : angle 0.60791 (50477) hydrogen bonds : bond 0.04053 ( 2048) hydrogen bonds : angle 4.31533 ( 6024) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 444 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 242 LYS cc_start: 0.7743 (mtpt) cc_final: 0.7018 (mmpt) REVERT: D 446 LEU cc_start: 0.7834 (tt) cc_final: 0.7455 (mp) REVERT: D 476 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: D 657 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7428 (mtm-85) REVERT: E 40 PHE cc_start: 0.7989 (m-10) cc_final: 0.7782 (m-10) REVERT: E 89 GLU cc_start: 0.7631 (mm-30) cc_final: 0.6801 (mm-30) REVERT: E 452 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6090 (ptt-90) REVERT: E 522 MET cc_start: 0.7206 (mtt) cc_final: 0.6552 (ptt) REVERT: E 580 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7660 (mmtm) REVERT: F 89 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7944 (mm-30) REVERT: F 141 TYR cc_start: 0.8965 (t80) cc_final: 0.8279 (t80) REVERT: F 165 TYR cc_start: 0.8561 (p90) cc_final: 0.8130 (p90) REVERT: F 367 MET cc_start: 0.8918 (mpp) cc_final: 0.8529 (mpp) REVERT: F 658 TYR cc_start: 0.8739 (m-80) cc_final: 0.8517 (m-80) REVERT: G 214 SER cc_start: 0.8140 (t) cc_final: 0.7614 (p) REVERT: G 459 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7880 (mm-30) REVERT: H 97 MET cc_start: 0.7173 (ptm) cc_final: 0.6964 (ptt) REVERT: H 105 ASP cc_start: 0.8211 (m-30) cc_final: 0.7939 (m-30) REVERT: H 684 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: H 700 LYS cc_start: 0.7648 (mppt) cc_final: 0.7244 (mtpt) REVERT: A 214 SER cc_start: 0.8268 (t) cc_final: 0.7861 (m) REVERT: A 324 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8915 (mp0) REVERT: A 347 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8883 (pmm) REVERT: B 101 LYS cc_start: 0.7293 (ttmt) cc_final: 0.6499 (tptm) REVERT: B 218 LYS cc_start: 0.8467 (mtmt) cc_final: 0.7868 (mmtm) REVERT: C 410 ARG cc_start: 0.7117 (ttm-80) cc_final: 0.6896 (ttm-80) REVERT: C 420 ASN cc_start: 0.7591 (m-40) cc_final: 0.6462 (p0) REVERT: C 447 PHE cc_start: 0.7516 (m-80) cc_final: 0.7177 (t80) REVERT: C 459 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7865 (mm-30) REVERT: C 540 MET cc_start: 0.8762 (mtm) cc_final: 0.8557 (mtt) REVERT: C 594 MET cc_start: 0.8352 (mtp) cc_final: 0.8137 (mpp) REVERT: C 658 TYR cc_start: 0.8695 (m-80) cc_final: 0.8262 (m-80) outliers start: 52 outliers final: 11 residues processed: 468 average time/residue: 0.7156 time to fit residues: 406.1495 Evaluate side-chains 387 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 371 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain G residue 452 ARG Chi-restraints excluded: chain G residue 594 MET Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 684 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 611 GLN Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 689 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 197 optimal weight: 6.9990 chunk 250 optimal weight: 20.0000 chunk 452 optimal weight: 6.9990 chunk 430 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 353 optimal weight: 4.9990 chunk 423 optimal weight: 30.0000 chunk 454 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 671 ASN E 611 GLN H 611 GLN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.208305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134279 restraints weight = 38257.286| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.12 r_work: 0.3196 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 37249 Z= 0.266 Angle : 0.721 10.699 50477 Z= 0.354 Chirality : 0.049 0.194 6001 Planarity : 0.005 0.079 6425 Dihedral : 9.919 172.321 5125 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.32 % Allowed : 7.79 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 0.79 (0.12), residues: 4649 helix: 1.71 (0.11), residues: 2259 sheet: 1.05 (0.18), residues: 762 loop : -1.51 (0.14), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 667 TYR 0.051 0.002 TYR E 708 PHE 0.022 0.002 PHE G 447 TRP 0.016 0.003 TRP F 477 HIS 0.006 0.001 HIS D 622 Details of bonding type rmsd covalent geometry : bond 0.00651 (37249) covalent geometry : angle 0.72073 (50477) hydrogen bonds : bond 0.05142 ( 2048) hydrogen bonds : angle 4.45592 ( 6024) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 379 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 122 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8090 (ttt180) REVERT: D 127 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8352 (mm) REVERT: D 165 TYR cc_start: 0.7936 (p90) cc_final: 0.7555 (p90) REVERT: D 242 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7471 (mmpt) REVERT: D 446 LEU cc_start: 0.7941 (tt) cc_final: 0.7498 (mp) REVERT: D 476 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: D 523 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7297 (pm20) REVERT: D 657 ARG cc_start: 0.7980 (mtm-85) cc_final: 0.7433 (mtm-85) REVERT: E 89 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7262 (mm-30) REVERT: E 452 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6642 (ptt180) REVERT: E 456 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: E 522 MET cc_start: 0.7272 (mtt) cc_final: 0.6740 (ptt) REVERT: E 580 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7896 (mmtm) REVERT: F 89 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8048 (mm-30) REVERT: F 141 TYR cc_start: 0.8972 (t80) cc_final: 0.8454 (t80) REVERT: F 165 TYR cc_start: 0.8669 (p90) cc_final: 0.8249 (p90) REVERT: F 444 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7476 (mp) REVERT: F 658 TYR cc_start: 0.8740 (m-80) cc_final: 0.7955 (m-80) REVERT: G 137 ILE cc_start: 0.8914 (mt) cc_final: 0.8572 (mm) REVERT: G 684 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: H 459 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7799 (mm-30) REVERT: H 684 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: A 207 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7467 (pp) REVERT: A 214 SER cc_start: 0.8331 (t) cc_final: 0.7945 (m) REVERT: A 324 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8862 (mp0) REVERT: B 101 LYS cc_start: 0.7618 (ttmt) cc_final: 0.6826 (tptp) REVERT: B 218 LYS cc_start: 0.8445 (mtmt) cc_final: 0.7981 (mmtm) REVERT: C 420 ASN cc_start: 0.7878 (m-40) cc_final: 0.6853 (p0) REVERT: C 447 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7321 (t80) REVERT: C 459 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7948 (mm-30) REVERT: C 707 ARG cc_start: 0.6032 (mmm160) cc_final: 0.4991 (tpt-90) outliers start: 93 outliers final: 37 residues processed: 423 average time/residue: 0.6163 time to fit residues: 317.8832 Evaluate side-chains 402 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 353 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 410 ARG Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 456 GLU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 306 MET Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 452 ARG Chi-restraints excluded: chain G residue 594 MET Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 672 THR Chi-restraints excluded: chain H residue 681 LYS Chi-restraints excluded: chain H residue 684 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 611 GLN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 680 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 91 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 304 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 366 optimal weight: 6.9990 chunk 322 optimal weight: 50.0000 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 374 optimal weight: 4.9990 chunk 411 optimal weight: 0.1980 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 611 GLN F 314 GLN A 276 GLN A 277 GLN A 293 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.210880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.125528 restraints weight = 38365.480| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.87 r_work: 0.3134 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 37249 Z= 0.146 Angle : 0.598 16.077 50477 Z= 0.292 Chirality : 0.044 0.176 6001 Planarity : 0.004 0.058 6425 Dihedral : 9.253 164.525 5123 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.17 % Allowed : 9.31 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 1.05 (0.12), residues: 4649 helix: 1.98 (0.11), residues: 2266 sheet: 1.24 (0.18), residues: 731 loop : -1.46 (0.13), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 21 TYR 0.027 0.001 TYR F 708 PHE 0.020 0.002 PHE G 447 TRP 0.008 0.001 TRP D 477 HIS 0.002 0.001 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00347 (37249) covalent geometry : angle 0.59842 (50477) hydrogen bonds : bond 0.04024 ( 2048) hydrogen bonds : angle 4.14627 ( 6024) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 387 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 127 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8153 (mm) REVERT: D 165 TYR cc_start: 0.7543 (p90) cc_final: 0.7149 (p90) REVERT: D 242 LYS cc_start: 0.7753 (mtpt) cc_final: 0.7045 (mmpt) REVERT: D 324 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8654 (mp0) REVERT: D 347 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8727 (ppp) REVERT: D 348 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.9058 (pm20) REVERT: D 446 LEU cc_start: 0.7734 (tt) cc_final: 0.7321 (mp) REVERT: D 476 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: D 523 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7634 (pm20) REVERT: D 657 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7417 (mtm-85) REVERT: E 452 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6323 (ptt180) REVERT: E 522 MET cc_start: 0.7244 (mtt) cc_final: 0.6489 (ptt) REVERT: E 580 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7628 (mmtm) REVERT: F 89 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7954 (mm-30) REVERT: F 141 TYR cc_start: 0.8883 (t80) cc_final: 0.8428 (t80) REVERT: F 165 TYR cc_start: 0.8653 (p90) cc_final: 0.8277 (p90) REVERT: F 367 MET cc_start: 0.8831 (mpp) cc_final: 0.8627 (mpp) REVERT: F 410 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7812 (ttp-110) REVERT: F 444 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7288 (mp) REVERT: F 658 TYR cc_start: 0.8758 (m-80) cc_final: 0.8519 (m-80) REVERT: F 680 MET cc_start: 0.9005 (mmm) cc_final: 0.8798 (mmt) REVERT: G 137 ILE cc_start: 0.8586 (mt) cc_final: 0.8277 (mm) REVERT: G 459 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7890 (mm-30) REVERT: G 684 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: H 444 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7420 (mp) REVERT: H 459 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7777 (mm-30) REVERT: H 597 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7425 (t0) REVERT: H 674 LYS cc_start: 0.8517 (tptt) cc_final: 0.7722 (ttpp) REVERT: A 214 SER cc_start: 0.8135 (t) cc_final: 0.7800 (m) REVERT: A 324 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8915 (mp0) REVERT: A 459 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7666 (mp0) REVERT: B 101 LYS cc_start: 0.7359 (ttmt) cc_final: 0.6540 (tptm) REVERT: B 218 LYS cc_start: 0.8402 (mtmt) cc_final: 0.7861 (mmtm) REVERT: C 410 ARG cc_start: 0.7297 (ttm-80) cc_final: 0.6878 (ttm-80) REVERT: C 420 ASN cc_start: 0.7712 (m-40) cc_final: 0.6618 (p0) REVERT: C 447 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.7176 (t80) REVERT: C 459 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7909 (mm-30) REVERT: C 658 TYR cc_start: 0.8706 (m-80) cc_final: 0.8278 (m-80) REVERT: C 707 ARG cc_start: 0.6010 (mmm160) cc_final: 0.4706 (tpt-90) outliers start: 87 outliers final: 32 residues processed: 433 average time/residue: 0.6085 time to fit residues: 320.3336 Evaluate side-chains 398 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 353 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 680 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 410 ARG Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain F residue 259 ASN Chi-restraints excluded: chain F residue 306 MET Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 452 ARG Chi-restraints excluded: chain G residue 594 MET Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 452 ARG Chi-restraints excluded: chain H residue 597 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 611 GLN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 680 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 363 optimal weight: 0.8980 chunk 260 optimal weight: 50.0000 chunk 264 optimal weight: 8.9990 chunk 283 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 368 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 437 optimal weight: 20.0000 chunk 421 optimal weight: 10.0000 chunk 430 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN E 611 GLN A 259 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN C 259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.208169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135191 restraints weight = 38259.833| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.91 r_work: 0.3178 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 37249 Z= 0.267 Angle : 0.714 14.520 50477 Z= 0.348 Chirality : 0.049 0.280 6001 Planarity : 0.005 0.053 6425 Dihedral : 10.013 172.536 5123 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 2.66 % Allowed : 10.38 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 0.75 (0.12), residues: 4649 helix: 1.69 (0.11), residues: 2259 sheet: 1.04 (0.18), residues: 735 loop : -1.49 (0.13), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 667 TYR 0.026 0.002 TYR E 708 PHE 0.020 0.002 PHE E 604 TRP 0.014 0.003 TRP C 477 HIS 0.005 0.001 HIS D 622 Details of bonding type rmsd covalent geometry : bond 0.00657 (37249) covalent geometry : angle 0.71429 (50477) hydrogen bonds : bond 0.05024 ( 2048) hydrogen bonds : angle 4.36985 ( 6024) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 356 time to evaluate : 1.482 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: D 122 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8152 (ttt180) REVERT: D 127 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8377 (mm) REVERT: D 165 TYR cc_start: 0.7714 (p90) cc_final: 0.7387 (p90) REVERT: D 242 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7518 (mmpt) REVERT: D 324 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8639 (mp0) REVERT: D 347 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8478 (ppp) REVERT: D 348 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8872 (pm20) REVERT: D 446 LEU cc_start: 0.7955 (tt) cc_final: 0.7483 (mp) REVERT: D 476 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: D 523 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: D 657 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7434 (mtm-85) REVERT: E 260 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7697 (mp) REVERT: E 452 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6448 (ptt180) REVERT: E 522 MET cc_start: 0.7330 (mtt) cc_final: 0.6789 (ptt) REVERT: F 89 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8044 (mm-30) REVERT: F 141 TYR cc_start: 0.8860 (t80) cc_final: 0.8449 (t80) REVERT: F 165 TYR cc_start: 0.8738 (p90) cc_final: 0.8441 (p90) REVERT: F 410 ARG cc_start: 0.8199 (ttp80) cc_final: 0.7973 (ttp-110) REVERT: F 444 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7533 (mp) REVERT: F 658 TYR cc_start: 0.8780 (m-80) cc_final: 0.8027 (m-80) REVERT: G 137 ILE cc_start: 0.8859 (mt) cc_final: 0.8534 (mm) REVERT: G 684 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8024 (tm-30) REVERT: H 459 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7812 (mm-30) REVERT: H 597 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7472 (t0) REVERT: H 674 LYS cc_start: 0.8590 (tptt) cc_final: 0.7953 (ttpp) REVERT: H 684 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: A 23 ILE cc_start: 0.7988 (mm) cc_final: 0.7670 (mp) REVERT: A 207 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7461 (pp) REVERT: A 214 SER cc_start: 0.8240 (t) cc_final: 0.7912 (m) REVERT: A 259 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7350 (m-40) REVERT: A 324 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8823 (mp0) REVERT: A 347 MET cc_start: 0.9042 (pmm) cc_final: 0.8837 (pmm) REVERT: A 372 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8296 (pm20) REVERT: B 101 LYS cc_start: 0.7643 (ttmt) cc_final: 0.6859 (tptm) REVERT: B 680 MET cc_start: 0.8935 (mmm) cc_final: 0.8727 (mtt) REVERT: C 128 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8274 (mpp) REVERT: C 242 LYS cc_start: 0.7948 (mtmm) cc_final: 0.7587 (mttp) REVERT: C 420 ASN cc_start: 0.7920 (m-40) cc_final: 0.6921 (p0) REVERT: C 447 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7335 (t80) REVERT: C 452 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6896 (ttp-170) REVERT: C 459 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7969 (mm-30) REVERT: C 707 ARG cc_start: 0.6338 (mmm160) cc_final: 0.5046 (tpt-90) outliers start: 107 outliers final: 47 residues processed: 421 average time/residue: 0.5751 time to fit residues: 295.1250 Evaluate side-chains 405 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 338 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 680 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 410 ARG Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 259 ASN Chi-restraints excluded: chain F residue 306 MET Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain F residue 700 LYS Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 452 ARG Chi-restraints excluded: chain G residue 594 MET Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 597 ASP Chi-restraints excluded: chain H residue 684 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 611 GLN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 680 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 338 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 315 optimal weight: 30.0000 chunk 93 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 424 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 382 optimal weight: 0.0030 chunk 298 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 449 optimal weight: 1.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.210310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.129118 restraints weight = 38318.334| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.70 r_work: 0.3129 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 37249 Z= 0.145 Angle : 0.612 16.284 50477 Z= 0.294 Chirality : 0.044 0.180 6001 Planarity : 0.004 0.047 6425 Dihedral : 9.336 167.105 5123 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.14 % Allowed : 11.25 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 1.06 (0.12), residues: 4649 helix: 1.97 (0.11), residues: 2264 sheet: 1.14 (0.18), residues: 729 loop : -1.38 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 21 TYR 0.029 0.001 TYR D 141 PHE 0.018 0.002 PHE G 447 TRP 0.008 0.001 TRP D 477 HIS 0.003 0.000 HIS D 571 Details of bonding type rmsd covalent geometry : bond 0.00345 (37249) covalent geometry : angle 0.61195 (50477) hydrogen bonds : bond 0.03974 ( 2048) hydrogen bonds : angle 4.12900 ( 6024) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 369 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 165 TYR cc_start: 0.7424 (p90) cc_final: 0.7014 (p90) REVERT: D 242 LYS cc_start: 0.7740 (mtpt) cc_final: 0.7049 (mmpt) REVERT: D 324 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8727 (mp0) REVERT: D 347 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8612 (ppp) REVERT: D 348 GLU cc_start: 0.9347 (OUTLIER) cc_final: 0.8965 (pm20) REVERT: D 446 LEU cc_start: 0.7706 (tt) cc_final: 0.7279 (mp) REVERT: D 476 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: D 523 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7718 (pm20) REVERT: D 657 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7500 (mtm-85) REVERT: E 124 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8869 (mm) REVERT: E 452 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6184 (ptt180) REVERT: E 522 MET cc_start: 0.7276 (mtt) cc_final: 0.6436 (ptt) REVERT: F 89 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7914 (mm-30) REVERT: F 141 TYR cc_start: 0.8818 (t80) cc_final: 0.8453 (t80) REVERT: F 165 TYR cc_start: 0.8698 (p90) cc_final: 0.8392 (p90) REVERT: F 410 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7800 (ttp-110) REVERT: F 444 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7316 (mp) REVERT: F 658 TYR cc_start: 0.8767 (m-80) cc_final: 0.8554 (m-80) REVERT: G 137 ILE cc_start: 0.8560 (mt) cc_final: 0.8237 (mm) REVERT: G 214 SER cc_start: 0.8057 (t) cc_final: 0.7465 (p) REVERT: G 523 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7854 (mm-30) REVERT: G 684 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: H 217 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8069 (tt) REVERT: H 225 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6768 (pt) REVERT: H 414 ASN cc_start: 0.8216 (p0) cc_final: 0.7874 (m110) REVERT: H 459 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7706 (mm-30) REVERT: H 597 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7359 (t0) REVERT: H 657 ARG cc_start: 0.8008 (mtt180) cc_final: 0.7734 (mtm-85) REVERT: H 674 LYS cc_start: 0.8553 (tptt) cc_final: 0.7839 (ttpp) REVERT: H 700 LYS cc_start: 0.7720 (mppt) cc_final: 0.7163 (mtpt) REVERT: A 23 ILE cc_start: 0.7782 (mm) cc_final: 0.7540 (mp) REVERT: A 58 ASP cc_start: 0.8400 (p0) cc_final: 0.8193 (p0) REVERT: A 207 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7319 (pp) REVERT: A 214 SER cc_start: 0.8082 (t) cc_final: 0.7768 (m) REVERT: A 324 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8932 (mp0) REVERT: A 347 MET cc_start: 0.9161 (pmm) cc_final: 0.8914 (pmm) REVERT: A 367 MET cc_start: 0.8993 (mpp) cc_final: 0.8756 (pmm) REVERT: A 372 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: A 459 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7635 (mp0) REVERT: B 101 LYS cc_start: 0.7354 (ttmt) cc_final: 0.6540 (tptm) REVERT: B 218 LYS cc_start: 0.8417 (mtmt) cc_final: 0.7898 (mmtm) REVERT: C 128 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8165 (mpp) REVERT: C 235 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8748 (m) REVERT: C 420 ASN cc_start: 0.7749 (m-40) cc_final: 0.6669 (p0) REVERT: C 447 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.7260 (t80) REVERT: C 459 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7892 (mm-30) REVERT: C 707 ARG cc_start: 0.6112 (mmm160) cc_final: 0.4622 (tpt-90) outliers start: 86 outliers final: 40 residues processed: 421 average time/residue: 0.6810 time to fit residues: 347.9364 Evaluate side-chains 406 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 348 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 680 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 410 ARG Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 259 ASN Chi-restraints excluded: chain F residue 306 MET Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain F residue 686 SER Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 452 ARG Chi-restraints excluded: chain G residue 594 MET Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 452 ARG Chi-restraints excluded: chain H residue 597 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 680 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 456 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 423 optimal weight: 20.0000 chunk 250 optimal weight: 0.9980 chunk 413 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 370 optimal weight: 40.0000 chunk 459 optimal weight: 2.9990 chunk 330 optimal weight: 9.9990 chunk 224 optimal weight: 0.0370 chunk 30 optimal weight: 6.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 258 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.210552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.127489 restraints weight = 38400.768| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.19 r_work: 0.3180 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 37249 Z= 0.145 Angle : 0.611 16.534 50477 Z= 0.293 Chirality : 0.044 0.202 6001 Planarity : 0.004 0.067 6425 Dihedral : 9.195 164.880 5123 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.09 % Allowed : 11.77 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 1.15 (0.12), residues: 4649 helix: 2.06 (0.11), residues: 2267 sheet: 1.20 (0.18), residues: 721 loop : -1.35 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 21 TYR 0.022 0.001 TYR E 255 PHE 0.017 0.002 PHE G 447 TRP 0.008 0.001 TRP C 477 HIS 0.003 0.001 HIS D 622 Details of bonding type rmsd covalent geometry : bond 0.00345 (37249) covalent geometry : angle 0.61071 (50477) hydrogen bonds : bond 0.03958 ( 2048) hydrogen bonds : angle 4.09823 ( 6024) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 363 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 139 ARG cc_start: 0.7347 (tpt170) cc_final: 0.6745 (tpt170) REVERT: D 165 TYR cc_start: 0.7487 (p90) cc_final: 0.7117 (p90) REVERT: D 242 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7201 (mmpt) REVERT: D 324 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8730 (mp0) REVERT: D 347 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8638 (ppp) REVERT: D 348 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.8891 (pm20) REVERT: D 446 LEU cc_start: 0.7849 (tt) cc_final: 0.7398 (mp) REVERT: D 476 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: D 657 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7490 (mtm-85) REVERT: E 447 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7282 (t80) REVERT: E 452 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6273 (ptt180) REVERT: E 522 MET cc_start: 0.7325 (mtt) cc_final: 0.6576 (ptt) REVERT: F 89 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7957 (mm-30) REVERT: F 141 TYR cc_start: 0.8758 (t80) cc_final: 0.8501 (t80) REVERT: F 165 TYR cc_start: 0.8717 (p90) cc_final: 0.8405 (p90) REVERT: F 410 ARG cc_start: 0.8170 (ttp80) cc_final: 0.7885 (ttp-110) REVERT: F 444 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7468 (mp) REVERT: G 137 ILE cc_start: 0.8540 (mt) cc_final: 0.8216 (mm) REVERT: G 214 SER cc_start: 0.8206 (t) cc_final: 0.7633 (p) REVERT: G 523 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7827 (mm-30) REVERT: G 684 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: H 217 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8128 (tt) REVERT: H 225 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6666 (pt) REVERT: H 414 ASN cc_start: 0.8143 (p0) cc_final: 0.7933 (m110) REVERT: H 459 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7770 (mm-30) REVERT: H 597 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7389 (t0) REVERT: H 657 ARG cc_start: 0.7957 (mtt180) cc_final: 0.7708 (mtm-85) REVERT: H 674 LYS cc_start: 0.8581 (tptt) cc_final: 0.7963 (ttpp) REVERT: H 700 LYS cc_start: 0.7674 (mppt) cc_final: 0.7224 (mtpt) REVERT: A 23 ILE cc_start: 0.7931 (mm) cc_final: 0.7653 (mp) REVERT: A 58 ASP cc_start: 0.8329 (p0) cc_final: 0.8113 (p0) REVERT: A 207 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7345 (pp) REVERT: A 214 SER cc_start: 0.8157 (t) cc_final: 0.7887 (m) REVERT: A 324 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8923 (mp0) REVERT: A 347 MET cc_start: 0.9174 (pmm) cc_final: 0.8916 (pmm) REVERT: A 372 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8313 (pm20) REVERT: A 459 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7657 (mp0) REVERT: B 101 LYS cc_start: 0.7489 (ttmt) cc_final: 0.6695 (tptm) REVERT: B 218 LYS cc_start: 0.8440 (mtmt) cc_final: 0.7958 (mmtm) REVERT: C 128 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8174 (mpp) REVERT: C 235 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8770 (m) REVERT: C 410 ARG cc_start: 0.7273 (ttm-80) cc_final: 0.6988 (ttm-80) REVERT: C 420 ASN cc_start: 0.7810 (m-40) cc_final: 0.6742 (p0) REVERT: C 447 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7317 (t80) REVERT: C 459 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7936 (mm-30) REVERT: C 658 TYR cc_start: 0.8710 (m-80) cc_final: 0.8352 (m-80) REVERT: C 707 ARG cc_start: 0.6153 (mmm160) cc_final: 0.4797 (tpt-90) outliers start: 84 outliers final: 49 residues processed: 413 average time/residue: 0.6994 time to fit residues: 353.2036 Evaluate side-chains 420 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 354 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 680 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 410 ARG Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 259 ASN Chi-restraints excluded: chain F residue 306 MET Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain F residue 686 SER Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 452 ARG Chi-restraints excluded: chain G residue 594 MET Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 452 ARG Chi-restraints excluded: chain H residue 522 MET Chi-restraints excluded: chain H residue 573 MET Chi-restraints excluded: chain H residue 597 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 611 GLN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 680 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 400 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 406 optimal weight: 0.9980 chunk 294 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 364 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 258 GLN A 259 ASN A 408 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.210227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.123903 restraints weight = 38224.941| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.88 r_work: 0.3114 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 37249 Z= 0.162 Angle : 0.628 16.123 50477 Z= 0.301 Chirality : 0.045 0.216 6001 Planarity : 0.004 0.068 6425 Dihedral : 9.299 168.989 5123 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.22 % Allowed : 12.02 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 1.15 (0.12), residues: 4649 helix: 2.04 (0.11), residues: 2267 sheet: 1.22 (0.18), residues: 721 loop : -1.34 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 21 TYR 0.026 0.001 TYR A 141 PHE 0.017 0.002 PHE G 447 TRP 0.009 0.001 TRP C 477 HIS 0.003 0.001 HIS D 571 Details of bonding type rmsd covalent geometry : bond 0.00390 (37249) covalent geometry : angle 0.62774 (50477) hydrogen bonds : bond 0.04094 ( 2048) hydrogen bonds : angle 4.12838 ( 6024) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 359 time to evaluate : 0.982 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: D 139 ARG cc_start: 0.7224 (tpt170) cc_final: 0.6684 (tpt170) REVERT: D 165 TYR cc_start: 0.7398 (p90) cc_final: 0.7040 (p90) REVERT: D 242 LYS cc_start: 0.7768 (mtpt) cc_final: 0.7096 (mmpt) REVERT: D 446 LEU cc_start: 0.7757 (tt) cc_final: 0.7309 (mp) REVERT: D 462 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8206 (mt-10) REVERT: D 476 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: D 657 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7526 (mtm-85) REVERT: E 452 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6218 (ptt180) REVERT: E 522 MET cc_start: 0.7359 (mtt) cc_final: 0.6507 (ptt) REVERT: F 42 LEU cc_start: 0.7268 (tp) cc_final: 0.7068 (tp) REVERT: F 89 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8021 (mm-30) REVERT: F 141 TYR cc_start: 0.8707 (t80) cc_final: 0.8387 (t80) REVERT: F 410 ARG cc_start: 0.8192 (ttp80) cc_final: 0.7883 (ttp-110) REVERT: F 444 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7351 (mp) REVERT: G 137 ILE cc_start: 0.8439 (mt) cc_final: 0.8143 (mm) REVERT: G 214 SER cc_start: 0.8145 (t) cc_final: 0.7561 (p) REVERT: G 410 ARG cc_start: 0.7544 (ttt180) cc_final: 0.7329 (ttp80) REVERT: G 523 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7899 (mm-30) REVERT: G 684 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: H 217 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8084 (tt) REVERT: H 225 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6758 (pt) REVERT: H 414 ASN cc_start: 0.8112 (p0) cc_final: 0.7806 (m110) REVERT: H 459 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7734 (mm-30) REVERT: H 597 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7415 (t0) REVERT: H 657 ARG cc_start: 0.8005 (mtt180) cc_final: 0.7733 (mtm-85) REVERT: H 674 LYS cc_start: 0.8579 (tptt) cc_final: 0.7883 (ttpp) REVERT: H 684 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: H 700 LYS cc_start: 0.7657 (mppt) cc_final: 0.7186 (mtpt) REVERT: A 23 ILE cc_start: 0.7900 (mm) cc_final: 0.7623 (mp) REVERT: A 58 ASP cc_start: 0.8350 (p0) cc_final: 0.8136 (p0) REVERT: A 207 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7282 (pp) REVERT: A 214 SER cc_start: 0.8138 (t) cc_final: 0.7819 (m) REVERT: A 324 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8965 (mp0) REVERT: A 347 MET cc_start: 0.9216 (pmm) cc_final: 0.8940 (pmm) REVERT: A 367 MET cc_start: 0.8824 (pmm) cc_final: 0.8476 (pmm) REVERT: A 372 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8354 (pm20) REVERT: A 459 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7649 (mp0) REVERT: B 101 LYS cc_start: 0.7386 (ttmt) cc_final: 0.6569 (tptm) REVERT: C 235 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8758 (m) REVERT: C 410 ARG cc_start: 0.7206 (ttm-80) cc_final: 0.6880 (ttm-80) REVERT: C 420 ASN cc_start: 0.7767 (m-40) cc_final: 0.6702 (p0) REVERT: C 447 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7299 (t80) REVERT: C 459 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7913 (mm-30) REVERT: C 707 ARG cc_start: 0.6142 (mmm160) cc_final: 0.4677 (tpt-90) outliers start: 89 outliers final: 56 residues processed: 418 average time/residue: 0.6962 time to fit residues: 353.7070 Evaluate side-chains 421 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 351 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 141 TYR Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 680 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 410 ARG Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 306 MET Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain F residue 686 SER Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 452 ARG Chi-restraints excluded: chain G residue 594 MET Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 452 ARG Chi-restraints excluded: chain H residue 522 MET Chi-restraints excluded: chain H residue 573 MET Chi-restraints excluded: chain H residue 597 ASP Chi-restraints excluded: chain H residue 684 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 611 GLN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 680 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 342 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 211 optimal weight: 9.9990 chunk 240 optimal weight: 9.9990 chunk 417 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 320 optimal weight: 40.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 258 GLN A 259 ASN A 408 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.209259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123740 restraints weight = 38329.122| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.78 r_work: 0.3101 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 37249 Z= 0.213 Angle : 0.676 16.486 50477 Z= 0.325 Chirality : 0.047 0.264 6001 Planarity : 0.004 0.074 6425 Dihedral : 9.610 171.307 5123 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.81 % Favored : 96.17 % Rotamer: Outliers : 2.02 % Allowed : 12.27 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 1.00 (0.12), residues: 4649 helix: 1.90 (0.11), residues: 2263 sheet: 1.15 (0.18), residues: 721 loop : -1.39 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 21 TYR 0.038 0.002 TYR D 141 PHE 0.017 0.002 PHE E 604 TRP 0.011 0.002 TRP C 477 HIS 0.004 0.001 HIS D 571 Details of bonding type rmsd covalent geometry : bond 0.00522 (37249) covalent geometry : angle 0.67561 (50477) hydrogen bonds : bond 0.04488 ( 2048) hydrogen bonds : angle 4.21967 ( 6024) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 355 time to evaluate : 1.618 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: D 128 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8147 (mpp) REVERT: D 139 ARG cc_start: 0.7602 (tpt170) cc_final: 0.6907 (tpt170) REVERT: D 242 LYS cc_start: 0.7863 (mtpt) cc_final: 0.7205 (mmpt) REVERT: D 446 LEU cc_start: 0.7796 (tt) cc_final: 0.7322 (mp) REVERT: D 462 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8261 (mt-10) REVERT: D 476 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: D 657 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7485 (mtm-85) REVERT: E 452 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6312 (ptt180) REVERT: E 522 MET cc_start: 0.7401 (mtt) cc_final: 0.6536 (ptt) REVERT: F 89 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8022 (mm-30) REVERT: F 141 TYR cc_start: 0.8715 (t80) cc_final: 0.8435 (t80) REVERT: F 410 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7890 (ttp-110) REVERT: F 444 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7409 (mp) REVERT: G 137 ILE cc_start: 0.8478 (mt) cc_final: 0.8156 (mm) REVERT: G 214 SER cc_start: 0.8137 (t) cc_final: 0.7524 (p) REVERT: G 215 ASP cc_start: 0.8212 (m-30) cc_final: 0.7703 (m-30) REVERT: G 410 ARG cc_start: 0.7546 (ttt180) cc_final: 0.7302 (ttp80) REVERT: G 523 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7898 (mm-30) REVERT: G 684 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: H 225 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6733 (pt) REVERT: H 414 ASN cc_start: 0.8141 (p0) cc_final: 0.7826 (m110) REVERT: H 597 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7466 (t0) REVERT: H 657 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7733 (mtm-85) REVERT: H 674 LYS cc_start: 0.8593 (tptt) cc_final: 0.7961 (tmmt) REVERT: H 700 LYS cc_start: 0.7684 (mppt) cc_final: 0.7211 (mtpt) REVERT: A 23 ILE cc_start: 0.7971 (mm) cc_final: 0.7675 (mp) REVERT: A 58 ASP cc_start: 0.8361 (p0) cc_final: 0.8140 (p0) REVERT: A 207 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7351 (pp) REVERT: A 214 SER cc_start: 0.8170 (t) cc_final: 0.7824 (m) REVERT: A 324 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8945 (mp0) REVERT: A 347 MET cc_start: 0.9208 (pmm) cc_final: 0.8927 (pmm) REVERT: A 367 MET cc_start: 0.8876 (pmm) cc_final: 0.8485 (pmm) REVERT: A 372 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8316 (pm20) REVERT: A 459 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7690 (mp0) REVERT: B 101 LYS cc_start: 0.7432 (ttmt) cc_final: 0.6623 (tptm) REVERT: C 124 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8008 (tm) REVERT: C 128 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7636 (mpp) REVERT: C 235 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8804 (m) REVERT: C 242 LYS cc_start: 0.7761 (mtmm) cc_final: 0.7411 (mttp) REVERT: C 410 ARG cc_start: 0.7251 (ttm-80) cc_final: 0.6898 (ttm-80) REVERT: C 420 ASN cc_start: 0.7821 (m-40) cc_final: 0.6765 (p0) REVERT: C 447 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.7285 (t80) REVERT: C 459 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7935 (mm-30) REVERT: C 707 ARG cc_start: 0.6223 (mmm160) cc_final: 0.4716 (tpt-90) outliers start: 81 outliers final: 49 residues processed: 409 average time/residue: 0.6986 time to fit residues: 348.5511 Evaluate side-chains 413 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 349 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 516 SER Chi-restraints excluded: chain D residue 669 GLU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 410 ARG Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 306 MET Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain F residue 686 SER Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 452 ARG Chi-restraints excluded: chain G residue 594 MET Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 452 ARG Chi-restraints excluded: chain H residue 516 SER Chi-restraints excluded: chain H residue 573 MET Chi-restraints excluded: chain H residue 597 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 611 GLN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 680 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 167 optimal weight: 0.0870 chunk 270 optimal weight: 0.0040 chunk 43 optimal weight: 1.9990 chunk 359 optimal weight: 8.9990 chunk 220 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 440 optimal weight: 9.9990 chunk 377 optimal weight: 5.9990 chunk 438 optimal weight: 0.0170 chunk 366 optimal weight: 5.9990 chunk 233 optimal weight: 0.8980 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN D 710 HIS ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.216324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.135837 restraints weight = 39823.155| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.44 r_work: 0.3438 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.130 37249 Z= 0.102 Angle : 0.579 16.899 50477 Z= 0.275 Chirality : 0.043 0.295 6001 Planarity : 0.003 0.050 6425 Dihedral : 8.443 144.210 5123 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.29 % Allowed : 13.07 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 1.39 (0.12), residues: 4649 helix: 2.28 (0.11), residues: 2261 sheet: 1.35 (0.18), residues: 730 loop : -1.30 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 21 TYR 0.024 0.001 TYR A 141 PHE 0.018 0.001 PHE G 447 TRP 0.004 0.001 TRP H 631 HIS 0.002 0.000 HIS E 710 Details of bonding type rmsd covalent geometry : bond 0.00224 (37249) covalent geometry : angle 0.57858 (50477) hydrogen bonds : bond 0.03281 ( 2048) hydrogen bonds : angle 3.93502 ( 6024) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9298 Ramachandran restraints generated. 4649 Oldfield, 0 Emsley, 4649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 380 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 127 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8143 (mm) REVERT: D 139 ARG cc_start: 0.7668 (tpt170) cc_final: 0.7047 (tpt170) REVERT: D 165 TYR cc_start: 0.7144 (p90) cc_final: 0.6848 (p90) REVERT: D 214 SER cc_start: 0.7835 (t) cc_final: 0.7472 (p) REVERT: D 242 LYS cc_start: 0.7552 (mtpt) cc_final: 0.6884 (mmpt) REVERT: D 324 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8653 (mp0) REVERT: D 446 LEU cc_start: 0.7788 (tt) cc_final: 0.7351 (mp) REVERT: D 657 ARG cc_start: 0.7998 (mtm-85) cc_final: 0.7317 (mtm-85) REVERT: D 707 ARG cc_start: 0.6257 (tpm170) cc_final: 0.5023 (mmt90) REVERT: E 89 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7240 (mm-30) REVERT: E 447 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7360 (t80) REVERT: E 522 MET cc_start: 0.7129 (mtt) cc_final: 0.6407 (ptt) REVERT: F 42 LEU cc_start: 0.7258 (tp) cc_final: 0.7050 (tp) REVERT: F 89 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7966 (mm-30) REVERT: F 255 TYR cc_start: 0.7814 (t80) cc_final: 0.7565 (t80) REVERT: F 410 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7831 (ttp-110) REVERT: G 137 ILE cc_start: 0.8524 (mt) cc_final: 0.8242 (mm) REVERT: G 214 SER cc_start: 0.8080 (t) cc_final: 0.7508 (p) REVERT: G 523 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7677 (mm-30) REVERT: H 97 MET cc_start: 0.6955 (ptm) cc_final: 0.6685 (ptt) REVERT: H 657 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7725 (mtm-85) REVERT: H 674 LYS cc_start: 0.8486 (tptt) cc_final: 0.7811 (ttpp) REVERT: H 700 LYS cc_start: 0.7553 (mppt) cc_final: 0.7133 (mtpt) REVERT: A 23 ILE cc_start: 0.7894 (mm) cc_final: 0.7651 (mp) REVERT: A 58 ASP cc_start: 0.8276 (p0) cc_final: 0.7983 (p0) REVERT: A 207 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7321 (pp) REVERT: A 214 SER cc_start: 0.8103 (t) cc_final: 0.7816 (m) REVERT: A 324 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8850 (mp0) REVERT: A 347 MET cc_start: 0.9103 (pmm) cc_final: 0.8848 (pmm) REVERT: A 367 MET cc_start: 0.8857 (pmm) cc_final: 0.8542 (pmm) REVERT: A 372 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8315 (pm20) REVERT: A 459 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7523 (mp0) REVERT: B 101 LYS cc_start: 0.7457 (ttmt) cc_final: 0.6632 (tptm) REVERT: B 218 LYS cc_start: 0.8390 (mtmt) cc_final: 0.7921 (mmtm) REVERT: B 707 ARG cc_start: 0.6179 (tpm170) cc_final: 0.4982 (tmm-80) REVERT: C 124 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8783 (tm) REVERT: C 225 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6298 (pp) REVERT: C 235 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8677 (m) REVERT: C 420 ASN cc_start: 0.7690 (m-40) cc_final: 0.6654 (p0) REVERT: C 447 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7332 (t80) REVERT: C 459 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7744 (mm-30) REVERT: C 658 TYR cc_start: 0.8684 (m-80) cc_final: 0.8359 (m-80) REVERT: C 707 ARG cc_start: 0.6099 (mmm160) cc_final: 0.4587 (tpt-90) outliers start: 52 outliers final: 21 residues processed: 416 average time/residue: 0.7088 time to fit residues: 358.7750 Evaluate side-chains 396 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 365 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 141 TYR Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 306 MET Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 680 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 301 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 380 optimal weight: 0.2980 chunk 414 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 270 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 430 optimal weight: 1.9990 chunk 331 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 611 GLN G 168 ASN A 259 ASN A 408 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.216393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.139429 restraints weight = 39527.995| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.64 r_work: 0.3428 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.130 37249 Z= 0.108 Angle : 0.593 17.139 50477 Z= 0.281 Chirality : 0.043 0.294 6001 Planarity : 0.003 0.091 6425 Dihedral : 8.143 135.503 5123 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.05 % Allowed : 13.74 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 1.52 (0.12), residues: 4649 helix: 2.39 (0.11), residues: 2252 sheet: 1.43 (0.18), residues: 730 loop : -1.23 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 21 TYR 0.024 0.001 TYR D 141 PHE 0.016 0.001 PHE G 447 TRP 0.004 0.001 TRP C 477 HIS 0.002 0.000 HIS E 710 Details of bonding type rmsd covalent geometry : bond 0.00244 (37249) covalent geometry : angle 0.59305 (50477) hydrogen bonds : bond 0.03386 ( 2048) hydrogen bonds : angle 3.92250 ( 6024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17564.24 seconds wall clock time: 298 minutes 48.12 seconds (17928.12 seconds total)