Starting phenix.real_space_refine on Mon Jul 6 06:20:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xi4_38370/07_2026/8xi4_38370.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xi4_38370/07_2026/8xi4_38370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xi4_38370/07_2026/8xi4_38370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xi4_38370/07_2026/8xi4_38370.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xi4_38370/07_2026/8xi4_38370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xi4_38370/07_2026/8xi4_38370.map" } resolution = 3.4 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 244 5.16 5 C 21320 2.51 5 N 5876 2.21 5 O 6324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 224 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33772 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3375 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 411} Chain: "B" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3300 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 32, 'TRANS': 387} Chain: "C" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1165 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "D" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3375 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 411} Chain: "E" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3300 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 32, 'TRANS': 387} Chain: "F" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1165 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "G" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3375 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 411} Chain: "H" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3300 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 32, 'TRANS': 387} Chain: "I" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1165 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "J" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3375 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 411} Chain: "K" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3300 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 32, 'TRANS': 387} Chain: "L" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1165 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "M" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 601 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "N" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 601 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "O" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 601 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "P" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 601 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 6.83, per 1000 atoms: 0.20 Number of scatterers: 33772 At special positions: 0 Unit cell: (175.5, 201.15, 214.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 244 16.00 O 6324 8.00 N 5876 7.00 C 21320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=84, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 272 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=2.03 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 103 " distance=1.87 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 217 " distance=2.50 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 414 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 260 " - pdb=" SG CYS D 272 " distance=1.89 Simple disulfide: pdb=" SG CYS D 302 " - pdb=" SG CYS D 377 " distance=2.03 Simple disulfide: pdb=" SG CYS D 307 " - pdb=" SG CYS D 381 " distance=2.03 Simple disulfide: pdb=" SG CYS D 329 " - pdb=" SG CYS D 371 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 27 " distance=2.03 Simple disulfide: pdb=" SG CYS E 89 " - pdb=" SG CYS E 103 " distance=2.03 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 199 " - pdb=" SG CYS E 223 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 217 " distance=2.50 Simple disulfide: pdb=" SG CYS E 393 " - pdb=" SG CYS E 414 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=1.72 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 260 " - pdb=" SG CYS G 272 " distance=2.03 Simple disulfide: pdb=" SG CYS G 302 " - pdb=" SG CYS G 377 " distance=2.03 Simple disulfide: pdb=" SG CYS G 307 " - pdb=" SG CYS G 381 " distance=2.03 Simple disulfide: pdb=" SG CYS G 329 " - pdb=" SG CYS G 371 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 27 " distance=2.03 Simple disulfide: pdb=" SG CYS H 89 " - pdb=" SG CYS H 103 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 263 " distance=2.03 Simple disulfide: pdb=" SG CYS H 199 " - pdb=" SG CYS H 223 " distance=2.03 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 217 " distance=2.50 Simple disulfide: pdb=" SG CYS H 393 " - pdb=" SG CYS H 414 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 260 " - pdb=" SG CYS J 272 " distance=2.03 Simple disulfide: pdb=" SG CYS J 302 " - pdb=" SG CYS J 377 " distance=2.03 Simple disulfide: pdb=" SG CYS J 307 " - pdb=" SG CYS J 381 " distance=2.16 Simple disulfide: pdb=" SG CYS J 329 " - pdb=" SG CYS J 371 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 122 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 27 " distance=2.03 Simple disulfide: pdb=" SG CYS K 89 " - pdb=" SG CYS K 103 " distance=2.03 Simple disulfide: pdb=" SG CYS K 150 " - pdb=" SG CYS K 263 " distance=1.72 Simple disulfide: pdb=" SG CYS K 199 " - pdb=" SG CYS K 223 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 217 " distance=2.50 Simple disulfide: pdb=" SG CYS K 393 " - pdb=" SG CYS K 414 " distance=2.03 Simple disulfide: pdb=" SG CYS M 33 " - pdb=" SG CYS M 45 " distance=2.03 Simple disulfide: pdb=" SG CYS M 40 " - pdb=" SG CYS M 58 " distance=2.04 Simple disulfide: pdb=" SG CYS M 52 " - pdb=" SG CYS M 67 " distance=2.03 Simple disulfide: pdb=" SG CYS M 72 " - pdb=" SG CYS M 84 " distance=2.03 Simple disulfide: pdb=" SG CYS M 79 " - pdb=" SG CYS M 97 " distance=2.03 Simple disulfide: pdb=" SG CYS M 91 " - pdb=" SG CYS M 108 " distance=2.03 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 45 " distance=2.03 Simple disulfide: pdb=" SG CYS N 40 " - pdb=" SG CYS N 58 " distance=2.04 Simple disulfide: pdb=" SG CYS N 52 " - pdb=" SG CYS N 67 " distance=2.03 Simple disulfide: pdb=" SG CYS N 72 " - pdb=" SG CYS N 84 " distance=2.03 Simple disulfide: pdb=" SG CYS N 79 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 108 " distance=2.03 Simple disulfide: pdb=" SG CYS O 33 " - pdb=" SG CYS O 45 " distance=2.03 Simple disulfide: pdb=" SG CYS O 40 " - pdb=" SG CYS O 58 " distance=2.04 Simple disulfide: pdb=" SG CYS O 52 " - pdb=" SG CYS O 67 " distance=2.03 Simple disulfide: pdb=" SG CYS O 72 " - pdb=" SG CYS O 84 " distance=2.03 Simple disulfide: pdb=" SG CYS O 79 " - pdb=" SG CYS O 97 " distance=2.03 Simple disulfide: pdb=" SG CYS O 91 " - pdb=" SG CYS O 108 " distance=2.03 Simple disulfide: pdb=" SG CYS P 33 " - pdb=" SG CYS P 45 " distance=2.03 Simple disulfide: pdb=" SG CYS P 40 " - pdb=" SG CYS P 58 " distance=2.04 Simple disulfide: pdb=" SG CYS P 52 " - pdb=" SG CYS P 67 " distance=2.03 Simple disulfide: pdb=" SG CYS P 72 " - pdb=" SG CYS P 84 " distance=2.03 Simple disulfide: pdb=" SG CYS P 79 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS P 91 " - pdb=" SG CYS P 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.4 seconds 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 92 sheets defined 12.6% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.990A pdb=" N SER A 115 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.545A pdb=" N VAL A 255 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.226A pdb=" N GLY A 259 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS A 260 " --> pdb=" O PRO A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.646A pdb=" N PHE A 288 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.641A pdb=" N THR A 294 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 441 removed outlier: 4.862A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 360 removed outlier: 3.763A pdb=" N VAL B 353 " --> pdb=" O PRO B 349 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL B 354 " --> pdb=" O HIS B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 395 removed outlier: 3.729A pdb=" N CYS B 369 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 4.368A pdb=" N LEU B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.834A pdb=" N MET C 170 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 171 " --> pdb=" O GLN C 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 167 through 171' Processing helix chain 'D' and resid 239 through 248 removed outlier: 3.591A pdb=" N LYS D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.837A pdb=" N PHE D 288 " --> pdb=" O ASP D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.882A pdb=" N THR D 294 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 441 removed outlier: 3.523A pdb=" N TRP D 410 " --> pdb=" O THR D 406 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 415 " --> pdb=" O ILE D 411 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 430 " --> pdb=" O LEU D 426 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 432 " --> pdb=" O ALA D 428 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 433 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS D 441 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 360 removed outlier: 3.801A pdb=" N VAL E 353 " --> pdb=" O PRO E 349 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL E 354 " --> pdb=" O HIS E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 399 removed outlier: 3.746A pdb=" N ILE E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 366 " --> pdb=" O LEU E 362 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR E 370 " --> pdb=" O ILE E 366 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE E 394 " --> pdb=" O ARG E 390 " (cutoff:3.500A) Proline residue: E 396 - end of helix removed outlier: 3.997A pdb=" N LEU E 399 " --> pdb=" O THR E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 removed outlier: 3.958A pdb=" N LEU E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU E 412 " --> pdb=" O LEU E 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 407 through 412' Processing helix chain 'F' and resid 145 through 150 removed outlier: 3.951A pdb=" N ALA F 150 " --> pdb=" O GLU F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 171 removed outlier: 4.030A pdb=" N MET F 170 " --> pdb=" O PRO F 167 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS F 171 " --> pdb=" O GLN F 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 167 through 171' Processing helix chain 'G' and resid 112 through 116 removed outlier: 4.202A pdb=" N SER G 115 " --> pdb=" O GLU G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 247 Processing helix chain 'G' and resid 251 through 255 Processing helix chain 'G' and resid 284 through 288 removed outlier: 3.588A pdb=" N ALA G 287 " --> pdb=" O PRO G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 411 Processing helix chain 'G' and resid 416 through 441 removed outlier: 3.619A pdb=" N VAL G 423 " --> pdb=" O SER G 419 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA G 428 " --> pdb=" O LEU G 424 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR G 429 " --> pdb=" O GLY G 425 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU G 434 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG G 440 " --> pdb=" O LEU G 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 360 removed outlier: 3.615A pdb=" N VAL H 353 " --> pdb=" O PRO H 349 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL H 354 " --> pdb=" O HIS H 350 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN H 358 " --> pdb=" O VAL H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 380 Processing helix chain 'H' and resid 385 through 399 removed outlier: 3.900A pdb=" N ILE H 394 " --> pdb=" O ARG H 390 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR H 395 " --> pdb=" O ASN H 391 " (cutoff:3.500A) Proline residue: H 396 - end of helix removed outlier: 3.876A pdb=" N LEU H 399 " --> pdb=" O THR H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 411 removed outlier: 3.679A pdb=" N LEU H 411 " --> pdb=" O ILE H 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 171 removed outlier: 3.668A pdb=" N MET I 170 " --> pdb=" O PRO I 167 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS I 171 " --> pdb=" O GLN I 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 167 through 171' Processing helix chain 'J' and resid 112 through 116 removed outlier: 4.042A pdb=" N SER J 115 " --> pdb=" O GLU J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 248 removed outlier: 3.804A pdb=" N LYS J 246 " --> pdb=" O GLU J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 256 Processing helix chain 'J' and resid 257 through 260 Processing helix chain 'J' and resid 284 through 288 removed outlier: 3.726A pdb=" N PHE J 288 " --> pdb=" O ASP J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 294 Processing helix chain 'J' and resid 404 through 441 removed outlier: 3.500A pdb=" N GLY J 425 " --> pdb=" O PHE J 421 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL J 432 " --> pdb=" O ALA J 428 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA J 433 " --> pdb=" O THR J 429 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU J 434 " --> pdb=" O ALA J 430 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL J 435 " --> pdb=" O VAL J 431 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG J 440 " --> pdb=" O LEU J 436 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS J 441 " --> pdb=" O PHE J 437 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 6 Processing helix chain 'K' and resid 348 through 360 removed outlier: 3.520A pdb=" N VAL K 353 " --> pdb=" O PRO K 349 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL K 354 " --> pdb=" O HIS K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 392 removed outlier: 3.573A pdb=" N CYS K 369 " --> pdb=" O ILE K 365 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS K 371 " --> pdb=" O GLY K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 394 through 399 removed outlier: 3.541A pdb=" N LEU K 399 " --> pdb=" O THR K 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 151 removed outlier: 3.696A pdb=" N ALA L 150 " --> pdb=" O GLN L 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 51 No H-bonds generated for 'chain 'M' and resid 49 through 51' Processing helix chain 'M' and resid 61 through 65 removed outlier: 3.589A pdb=" N GLU M 64 " --> pdb=" O GLY M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 90 No H-bonds generated for 'chain 'M' and resid 88 through 90' Processing helix chain 'N' and resid 49 through 51 No H-bonds generated for 'chain 'N' and resid 49 through 51' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'O' and resid 49 through 51 No H-bonds generated for 'chain 'O' and resid 49 through 51' Processing helix chain 'O' and resid 61 through 65 Processing helix chain 'O' and resid 88 through 90 No H-bonds generated for 'chain 'O' and resid 88 through 90' Processing helix chain 'O' and resid 100 through 104 removed outlier: 3.686A pdb=" N GLU O 103 " --> pdb=" O GLY O 100 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER O 104 " --> pdb=" O SER O 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 100 through 104' Processing helix chain 'P' and resid 49 through 51 No H-bonds generated for 'chain 'P' and resid 49 through 51' Processing helix chain 'P' and resid 61 through 65 removed outlier: 3.787A pdb=" N LYS P 65 " --> pdb=" O SER P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 90 No H-bonds generated for 'chain 'P' and resid 88 through 90' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 3.614A pdb=" N VAL A 27 " --> pdb=" O VAL A 19 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 27 through 33 current: chain 'A' and resid 119 through 137 removed outlier: 3.720A pdb=" N VAL A 133 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 145 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR A 137 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N SER A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 140 through 148 current: chain 'A' and resid 184 through 187 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 184 through 187 current: chain 'A' and resid 215 through 216 Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.641A pdb=" N TYR A 107 " --> pdb=" O LYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 61 removed outlier: 3.773A pdb=" N THR A 101 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA6, first strand: chain 'A' and resid 297 through 307 removed outlier: 4.941A pdb=" N ASP A 299 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS A 322 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 316 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.702A pdb=" N VAL A 345 " --> pdb=" O CYS A 329 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS A 329 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA9, first strand: chain 'B' and resid 17 through 19 removed outlier: 3.626A pdb=" N ALA B 17 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 34 through 37 removed outlier: 4.776A pdb=" N VAL B 36 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG B 46 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 10.244A pdb=" N SER B 50 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N MET B 68 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR B 64 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.502A pdb=" N ASP B 107 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 153 Processing sheet with id=AB4, first strand: chain 'B' and resid 163 through 164 Processing sheet with id=AB5, first strand: chain 'B' and resid 166 through 167 Processing sheet with id=AB6, first strand: chain 'B' and resid 178 through 180 Processing sheet with id=AB7, first strand: chain 'B' and resid 204 through 208 removed outlier: 3.639A pdb=" N GLY B 207 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 272 through 275 Processing sheet with id=AB9, first strand: chain 'C' and resid 113 through 118 removed outlier: 4.554A pdb=" N GLY C 124 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU C 118 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 187 through 188 Processing sheet with id=AC2, first strand: chain 'C' and resid 215 through 217 removed outlier: 6.741A pdb=" N ILE C 216 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N VAL C 224 " --> pdb=" O TRP C 244 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TRP C 244 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE C 226 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER C 240 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AC4, first strand: chain 'D' and resid 15 through 19 removed outlier: 3.656A pdb=" N VAL D 27 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N MET D 132 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR D 36 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLN D 130 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 145 " --> pdb=" O VAL D 133 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 143 through 148 current: chain 'D' and resid 269 through 270 Processing sheet with id=AC5, first strand: chain 'D' and resid 41 through 48 removed outlier: 3.548A pdb=" N ASN D 43 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA D 121 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.696A pdb=" N TYR D 107 " --> pdb=" O LYS D 54 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AC8, first strand: chain 'D' and resid 204 through 206 Processing sheet with id=AC9, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AD1, first strand: chain 'D' and resid 297 through 306 removed outlier: 6.909A pdb=" N LEU D 300 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LYS D 322 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N CYS D 302 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA D 320 " --> pdb=" O CYS D 302 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE D 304 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR D 318 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU D 306 " --> pdb=" O ILE D 316 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 344 through 347 removed outlier: 3.905A pdb=" N VAL D 345 " --> pdb=" O CYS D 329 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS D 329 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS D 332 " --> pdb=" O GLN D 369 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AD4, first strand: chain 'E' and resid 17 through 18 removed outlier: 3.714A pdb=" N ALA E 17 " --> pdb=" O SER E 29 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 34 through 37 removed outlier: 3.524A pdb=" N GLN E 48 " --> pdb=" O GLU E 34 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL E 36 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG E 46 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 10.058A pdb=" N SER E 50 " --> pdb=" O MET E 68 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N MET E 68 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR E 64 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN E 69 " --> pdb=" O THR E 72 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 81 through 84 removed outlier: 4.572A pdb=" N ASP E 107 " --> pdb=" O HIS E 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 146 through 153 Processing sheet with id=AD8, first strand: chain 'E' and resid 234 through 235 Processing sheet with id=AD9, first strand: chain 'E' and resid 178 through 180 Processing sheet with id=AE1, first strand: chain 'E' and resid 204 through 208 removed outlier: 3.639A pdb=" N GLY E 207 " --> pdb=" O TYR E 197 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 272 through 276 removed outlier: 3.967A pdb=" N THR E 279 " --> pdb=" O LYS E 276 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 121 through 127 removed outlier: 5.213A pdb=" N VAL F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU F 118 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY F 124 " --> pdb=" O ILE F 116 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 186 through 187 Processing sheet with id=AE5, first strand: chain 'F' and resid 215 through 217 removed outlier: 6.562A pdb=" N ILE F 216 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N VAL F 224 " --> pdb=" O TRP F 244 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP F 244 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE F 226 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER F 240 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 2 through 8 removed outlier: 3.602A pdb=" N ALA G 5 " --> pdb=" O ILE G 279 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS G 161 " --> pdb=" O ASP G 282 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE G 157 " --> pdb=" O ALA G 160 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 14 through 21 removed outlier: 3.625A pdb=" N VAL G 27 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG G 21 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ALA G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU G 29 " --> pdb=" O TYR G 137 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR G 137 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE G 31 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE G 135 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU G 33 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL G 133 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN G 35 " --> pdb=" O ALA G 131 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA G 131 " --> pdb=" O ASN G 35 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ARG G 37 " --> pdb=" O VAL G 129 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL G 129 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE G 39 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY G 127 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA G 121 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE G 47 " --> pdb=" O ALA G 119 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA G 119 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL G 133 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA G 145 " --> pdb=" O VAL G 133 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 143 through 148 current: chain 'G' and resid 184 through 187 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 184 through 187 current: chain 'G' and resid 215 through 216 Processing sheet with id=AE8, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.636A pdb=" N TYR G 107 " --> pdb=" O LYS G 54 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 60 through 61 removed outlier: 3.637A pdb=" N PHE G 81 " --> pdb=" O GLN G 102 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AF2, first strand: chain 'G' and resid 261 through 262 Processing sheet with id=AF3, first strand: chain 'G' and resid 297 through 306 removed outlier: 6.986A pdb=" N LEU G 300 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LYS G 322 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N CYS G 302 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ALA G 320 " --> pdb=" O CYS G 302 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE G 304 " --> pdb=" O THR G 318 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR G 318 " --> pdb=" O ILE G 304 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE G 353 " --> pdb=" O VAL G 319 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 331 through 332 Processing sheet with id=AF5, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AF6, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=AF7, first strand: chain 'H' and resid 34 through 37 removed outlier: 3.535A pdb=" N GLN H 48 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL H 36 " --> pdb=" O ARG H 46 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG H 46 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 68 through 69 Processing sheet with id=AF9, first strand: chain 'H' and resid 81 through 84 removed outlier: 4.422A pdb=" N ASP H 107 " --> pdb=" O HIS H 126 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 146 through 153 Processing sheet with id=AG2, first strand: chain 'H' and resid 234 through 235 removed outlier: 3.664A pdb=" N GLY H 250 " --> pdb=" O MET H 166 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 178 through 180 Processing sheet with id=AG4, first strand: chain 'H' and resid 204 through 208 removed outlier: 3.638A pdb=" N GLY H 207 " --> pdb=" O TYR H 197 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 272 through 276 removed outlier: 3.758A pdb=" N THR H 279 " --> pdb=" O LYS H 276 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 114 through 118 removed outlier: 4.629A pdb=" N GLY I 124 " --> pdb=" O ILE I 116 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU I 118 " --> pdb=" O VAL I 122 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL I 122 " --> pdb=" O LEU I 118 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 128 through 129 removed outlier: 3.885A pdb=" N VAL I 129 " --> pdb=" O ARG I 132 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 186 through 188 Processing sheet with id=AG9, first strand: chain 'I' and resid 215 through 217 removed outlier: 9.866A pdb=" N VAL I 224 " --> pdb=" O TRP I 244 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N TRP I 244 " --> pdb=" O VAL I 224 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE I 226 " --> pdb=" O VAL I 242 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 2 through 8 Processing sheet with id=AH2, first strand: chain 'J' and resid 15 through 19 removed outlier: 6.396A pdb=" N MET J 132 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR J 36 " --> pdb=" O GLN J 130 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN J 130 " --> pdb=" O THR J 36 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TYR J 137 " --> pdb=" O SER J 141 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER J 141 " --> pdb=" O TYR J 137 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 184 through 186 removed outlier: 6.680A pdb=" N ALA J 119 " --> pdb=" O ILE J 47 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE J 47 " --> pdb=" O ALA J 119 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA J 121 " --> pdb=" O GLU J 45 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 51 through 54 Processing sheet with id=AH5, first strand: chain 'J' and resid 60 through 61 Processing sheet with id=AH6, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AH7, first strand: chain 'J' and resid 297 through 306 removed outlier: 5.733A pdb=" N ASP J 299 " --> pdb=" O LYS J 322 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS J 322 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE J 316 " --> pdb=" O THR J 305 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 344 through 347 removed outlier: 3.522A pdb=" N VAL J 345 " --> pdb=" O CYS J 329 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY J 327 " --> pdb=" O LEU J 347 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 388 through 389 Processing sheet with id=AI1, first strand: chain 'K' and resid 17 through 18 removed outlier: 3.547A pdb=" N ALA K 17 " --> pdb=" O SER K 29 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 34 through 37 removed outlier: 3.635A pdb=" N GLN K 48 " --> pdb=" O GLU K 34 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL K 36 " --> pdb=" O ARG K 46 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG K 46 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N SER K 50 " --> pdb=" O MET K 68 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET K 68 " --> pdb=" O SER K 50 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 81 through 84 removed outlier: 4.461A pdb=" N ASP K 107 " --> pdb=" O HIS K 126 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 146 through 153 removed outlier: 3.619A pdb=" N CYS K 150 " --> pdb=" O ALA K 261 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 163 through 164 Processing sheet with id=AI6, first strand: chain 'K' and resid 166 through 167 Processing sheet with id=AI7, first strand: chain 'K' and resid 178 through 180 Processing sheet with id=AI8, first strand: chain 'K' and resid 207 through 208 removed outlier: 3.638A pdb=" N GLY K 207 " --> pdb=" O TYR K 197 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'K' and resid 272 through 276 Processing sheet with id=AJ1, first strand: chain 'L' and resid 133 through 134 removed outlier: 5.298A pdb=" N VAL L 122 " --> pdb=" O LEU L 118 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU L 118 " --> pdb=" O VAL L 122 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY L 124 " --> pdb=" O ILE L 116 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 186 through 188 Processing sheet with id=AJ3, first strand: chain 'L' and resid 215 through 217 removed outlier: 6.678A pdb=" N ILE L 216 " --> pdb=" O VAL L 224 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ALA L 225 " --> pdb=" O TRP L 244 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N TRP L 244 " --> pdb=" O ALA L 225 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL L 227 " --> pdb=" O VAL L 242 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL L 242 " --> pdb=" O VAL L 227 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'M' and resid 37 through 39 Processing sheet with id=AJ5, first strand: chain 'M' and resid 76 through 78 Processing sheet with id=AJ6, first strand: chain 'N' and resid 37 through 39 Processing sheet with id=AJ7, first strand: chain 'N' and resid 76 through 78 Processing sheet with id=AJ8, first strand: chain 'O' and resid 37 through 39 Processing sheet with id=AJ9, first strand: chain 'O' and resid 76 through 78 Processing sheet with id=AK1, first strand: chain 'P' and resid 37 through 39 Processing sheet with id=AK2, first strand: chain 'P' and resid 76 through 78 839 hydrogen bonds defined for protein. 2172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.33 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10935 1.34 - 1.46: 7769 1.46 - 1.58: 15670 1.58 - 1.70: 2 1.70 - 1.83: 292 Bond restraints: 34668 Sorted by residual: bond pdb=" CB PRO F 183 " pdb=" CG PRO F 183 " ideal model delta sigma weight residual 1.492 1.631 -0.139 5.00e-02 4.00e+02 7.70e+00 bond pdb=" CA ALA J 5 " pdb=" C ALA J 5 " ideal model delta sigma weight residual 1.522 1.554 -0.033 1.24e-02 6.50e+03 6.90e+00 bond pdb=" N ALA H 40 " pdb=" CA ALA H 40 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.31e-02 5.83e+03 6.31e+00 bond pdb=" CB PRO D 22 " pdb=" CG PRO D 22 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.21e+00 bond pdb=" N ILE E 228 " pdb=" CA ILE E 228 " ideal model delta sigma weight residual 1.459 1.431 0.028 1.22e-02 6.72e+03 5.20e+00 ... (remaining 34663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 46433 2.66 - 5.31: 665 5.31 - 7.97: 95 7.97 - 10.63: 24 10.63 - 13.28: 7 Bond angle restraints: 47224 Sorted by residual: angle pdb=" O ILE K 228 " pdb=" C ILE K 228 " pdb=" N ASP K 229 " ideal model delta sigma weight residual 122.62 135.47 -12.85 1.40e+00 5.10e-01 8.42e+01 angle pdb=" CA ILE K 228 " pdb=" C ILE K 228 " pdb=" N ASP K 229 " ideal model delta sigma weight residual 116.45 103.17 13.28 1.46e+00 4.69e-01 8.28e+01 angle pdb=" N TYR G 93 " pdb=" CA TYR G 93 " pdb=" C TYR G 93 " ideal model delta sigma weight residual 111.36 120.79 -9.43 1.09e+00 8.42e-01 7.48e+01 angle pdb=" CA PRO F 183 " pdb=" N PRO F 183 " pdb=" CD PRO F 183 " ideal model delta sigma weight residual 112.00 100.56 11.44 1.40e+00 5.10e-01 6.68e+01 angle pdb=" N ALA J 310 " pdb=" CA ALA J 310 " pdb=" C ALA J 310 " ideal model delta sigma weight residual 110.23 120.69 -10.46 1.45e+00 4.76e-01 5.20e+01 ... (remaining 47219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 17840 18.02 - 36.04: 2236 36.04 - 54.06: 638 54.06 - 72.07: 123 72.07 - 90.09: 47 Dihedral angle restraints: 20884 sinusoidal: 8296 harmonic: 12588 Sorted by residual: dihedral pdb=" CB CYS J 63 " pdb=" SG CYS J 63 " pdb=" SG CYS J 96 " pdb=" CB CYS J 96 " ideal model delta sinusoidal sigma weight residual 93.00 6.61 86.39 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS M 72 " pdb=" SG CYS M 72 " pdb=" SG CYS M 84 " pdb=" CB CYS M 84 " ideal model delta sinusoidal sigma weight residual -86.00 -172.15 86.15 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 27 " pdb=" CB CYS B 27 " ideal model delta sinusoidal sigma weight residual -86.00 -171.89 85.89 1 1.00e+01 1.00e-02 8.91e+01 ... (remaining 20881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4399 0.067 - 0.133: 726 0.133 - 0.200: 68 0.200 - 0.266: 18 0.266 - 0.333: 9 Chirality restraints: 5220 Sorted by residual: chirality pdb=" CA TYR G 93 " pdb=" N TYR G 93 " pdb=" C TYR G 93 " pdb=" CB TYR G 93 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA ALA J 310 " pdb=" N ALA J 310 " pdb=" C ALA J 310 " pdb=" CB ALA J 310 " both_signs ideal model delta sigma weight residual False 2.48 2.15 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA GLU E 35 " pdb=" N GLU E 35 " pdb=" C GLU E 35 " pdb=" CB GLU E 35 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 5217 not shown) Planarity restraints: 6120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP E 348 " -0.077 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO E 349 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO E 349 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO E 349 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 21 " 0.074 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO D 22 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO D 22 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 22 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 309 " -0.021 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" C TYR A 309 " 0.071 2.00e-02 2.50e+03 pdb=" O TYR A 309 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA A 310 " -0.024 2.00e-02 2.50e+03 ... (remaining 6117 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 3 2.05 - 2.76: 4975 2.76 - 3.48: 41953 3.48 - 4.19: 73868 4.19 - 4.90: 130324 Nonbonded interactions: 251123 Sorted by model distance: nonbonded pdb=" OD1 ASP P 53 " pdb="CA CA P 201 " model vdw 1.341 3.250 nonbonded pdb=" CG ASP P 53 " pdb="CA CA P 201 " model vdw 1.961 3.480 nonbonded pdb=" OD2 ASP P 57 " pdb=" OD2 ASP P 63 " model vdw 2.023 3.040 nonbonded pdb=" OD1 ASP H 3 " pdb=" NZ LYS O 70 " model vdw 2.143 3.120 nonbonded pdb=" OD2 ASP O 96 " pdb="CA CA O 202 " model vdw 2.184 3.250 ... (remaining 251118 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.390 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 0.007 0.474 34752 Z= 0.340 Angle : 0.853 43.523 47392 Z= 0.480 Chirality : 0.052 0.333 5220 Planarity : 0.007 0.116 6120 Dihedral : 17.182 90.093 12568 Min Nonbonded Distance : 1.341 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.19 % Allowed : 29.97 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.11), residues: 4332 helix: -3.75 (0.13), residues: 376 sheet: -0.21 (0.17), residues: 1020 loop : -1.94 (0.10), residues: 2936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG G 143 TYR 0.013 0.001 TYR L 163 PHE 0.047 0.002 PHE A 437 TRP 0.021 0.001 TRP G 142 HIS 0.006 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (34668) covalent geometry : angle 0.79215 / 0.46 (47224) SS BOND : bond 0.11631 / 9.14 ( 84) SS BOND : angle 5.38893 / 4.05 ( 168) hydrogen bonds : bond 0.29557 / 20.17 ( 839) hydrogen bonds : angle 10.23057 / 7.08 ( 2172) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 445 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.8367 (tt0) cc_final: 0.8099 (tt0) REVERT: B 199 CYS cc_start: 0.6012 (m) cc_final: 0.5767 (m) REVERT: B 219 ASP cc_start: 0.6436 (t0) cc_final: 0.6171 (t0) REVERT: G 35 ASN cc_start: 0.8650 (m110) cc_final: 0.8427 (m110) REVERT: G 51 TYR cc_start: 0.9076 (p90) cc_final: 0.8824 (p90) REVERT: G 164 ILE cc_start: 0.8977 (mm) cc_final: 0.8728 (mm) REVERT: G 397 GLU cc_start: 0.8089 (tp30) cc_final: 0.7720 (tt0) REVERT: H 64 TYR cc_start: 0.7724 (m-80) cc_final: 0.7441 (m-80) REVERT: J 10 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7663 (mmmt) REVERT: K 194 GLN cc_start: 0.7886 (mp10) cc_final: 0.7167 (tt0) REVERT: K 201 CYS cc_start: 0.4505 (OUTLIER) cc_final: 0.3714 (t) REVERT: L 211 ASP cc_start: 0.8431 (m-30) cc_final: 0.8043 (m-30) outliers start: 7 outliers final: 0 residues processed: 450 average time/residue: 0.1925 time to fit residues: 140.7007 Evaluate side-chains 380 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 201 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 253 ASN B 5 HIS B 41 HIS B 168 GLN B 175 HIS ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 219 ASN E 168 GLN E 230 ASN E 253 HIS E 338 GLN E 391 ASN F 119 ASN ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 HIS F 194 GLN G 35 ASN G 226 GLN G 328 ASN G 343 ASN G 356 HIS G 369 GLN G 395 HIS ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 404 GLN I 119 ASN J 35 ASN J 439 HIS K 126 HIS K 155 HIS K 222 GLN L 119 ASN M 39 GLN M 83 GLN N 83 GLN O 83 GLN P 83 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.168566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.127297 restraints weight = 43949.596| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.33 r_work: 0.3034 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34752 Z= 0.136 Angle : 0.584 8.248 47392 Z= 0.309 Chirality : 0.045 0.243 5220 Planarity : 0.005 0.077 6120 Dihedral : 5.270 73.029 4705 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.20 % Allowed : 26.44 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.12), residues: 4332 helix: -1.41 (0.22), residues: 416 sheet: -0.18 (0.16), residues: 1100 loop : -1.75 (0.11), residues: 2816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 390 TYR 0.019 0.001 TYR A 309 PHE 0.018 0.001 PHE A 311 TRP 0.017 0.001 TRP L 188 HIS 0.005 0.001 HIS E 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (34668) covalent geometry : angle 0.58133 / 0.31 (47224) SS BOND : bond 0.00306 / 0.21 ( 84) SS BOND : angle 1.07816 / 0.79 ( 168) hydrogen bonds : bond 0.04913 / 3.25 ( 839) hydrogen bonds : angle 6.50173 / 4.49 ( 2172) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 400 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8656 (mmtp) REVERT: A 232 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8967 (t) REVERT: A 265 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7153 (tm-30) REVERT: B 174 ASP cc_start: 0.8508 (t0) cc_final: 0.8300 (t0) REVERT: B 219 ASP cc_start: 0.6554 (t0) cc_final: 0.6137 (t0) REVERT: D 226 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7509 (pp30) REVERT: D 265 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7645 (tp30) REVERT: D 309 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7138 (m-10) REVERT: E 165 GLU cc_start: 0.8699 (tt0) cc_final: 0.8412 (tt0) REVERT: E 221 LYS cc_start: 0.8541 (mptt) cc_final: 0.7740 (mtmt) REVERT: E 284 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9388 (mt) REVERT: E 305 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8602 (ttt-90) REVERT: G 164 ILE cc_start: 0.9055 (mm) cc_final: 0.8664 (mm) REVERT: G 397 GLU cc_start: 0.8642 (tp30) cc_final: 0.8340 (tt0) REVERT: H 64 TYR cc_start: 0.8178 (m-80) cc_final: 0.7726 (m-80) REVERT: H 205 ARG cc_start: 0.6612 (mtp85) cc_final: 0.6101 (mtm-85) REVERT: H 284 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9200 (mp) REVERT: I 185 PHE cc_start: 0.5326 (OUTLIER) cc_final: 0.5081 (m-10) REVERT: J 161 LYS cc_start: 0.8516 (mttm) cc_final: 0.8307 (ttpt) REVERT: J 414 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7155 (mp) REVERT: K 194 GLN cc_start: 0.7727 (mp10) cc_final: 0.7261 (mt0) REVERT: K 353 VAL cc_start: 0.9086 (t) cc_final: 0.8563 (m) REVERT: K 376 MET cc_start: 0.8007 (ttm) cc_final: 0.7664 (mmp) outliers start: 157 outliers final: 90 residues processed: 523 average time/residue: 0.1865 time to fit residues: 162.2785 Evaluate side-chains 478 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 378 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain O residue 63 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 416 optimal weight: 2.9990 chunk 344 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 339 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 129 optimal weight: 0.4980 chunk 158 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 GLN G 369 GLN ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 GLN H 230 ASN K 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.169534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.132771 restraints weight = 43567.423| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.99 r_work: 0.2921 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 34752 Z= 0.132 Angle : 0.567 10.402 47392 Z= 0.296 Chirality : 0.045 0.235 5220 Planarity : 0.005 0.066 6120 Dihedral : 5.141 72.902 4704 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.00 % Allowed : 26.12 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.12), residues: 4332 helix: -0.33 (0.26), residues: 416 sheet: -0.24 (0.16), residues: 1112 loop : -1.63 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 268 TYR 0.016 0.001 TYR A 309 PHE 0.013 0.001 PHE A 311 TRP 0.017 0.001 TRP L 188 HIS 0.004 0.001 HIS G 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (34668) covalent geometry : angle 0.56139 / 0.29 (47224) SS BOND : bond 0.00317 / 0.19 ( 84) SS BOND : angle 1.44058 / 1.00 ( 168) hydrogen bonds : bond 0.04177 / 2.76 ( 839) hydrogen bonds : angle 5.89303 / 4.05 ( 2172) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 387 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8055 (pttt) REVERT: A 123 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8604 (mmtp) REVERT: B 31 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8127 (tt) REVERT: B 160 GLN cc_start: 0.8684 (mp10) cc_final: 0.8177 (mp10) REVERT: C 259 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6471 (tp30) REVERT: D 99 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7945 (tm-30) REVERT: D 226 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7435 (pp30) REVERT: D 265 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7555 (tp30) REVERT: D 309 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7117 (m-80) REVERT: E 165 GLU cc_start: 0.8675 (tt0) cc_final: 0.8368 (tt0) REVERT: E 221 LYS cc_start: 0.8565 (mptt) cc_final: 0.7782 (mtmt) REVERT: E 305 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8551 (ttt-90) REVERT: E 362 LEU cc_start: 0.5033 (OUTLIER) cc_final: 0.4807 (pt) REVERT: F 236 ARG cc_start: 0.3086 (OUTLIER) cc_final: 0.2240 (mtm180) REVERT: G 164 ILE cc_start: 0.9048 (mm) cc_final: 0.8658 (mm) REVERT: G 397 GLU cc_start: 0.8608 (tp30) cc_final: 0.8321 (tt0) REVERT: H 64 TYR cc_start: 0.8270 (m-80) cc_final: 0.7881 (m-80) REVERT: H 205 ARG cc_start: 0.6714 (mtp85) cc_final: 0.6123 (mtm-85) REVERT: H 284 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9201 (mp) REVERT: I 185 PHE cc_start: 0.5467 (OUTLIER) cc_final: 0.5159 (m-10) REVERT: K 194 GLN cc_start: 0.7700 (mp10) cc_final: 0.7218 (mt0) REVERT: K 229 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.6949 (t0) REVERT: K 376 MET cc_start: 0.7899 (ttm) cc_final: 0.7578 (mmp) REVERT: L 200 PHE cc_start: 0.5285 (t80) cc_final: 0.5033 (t80) outliers start: 187 outliers final: 133 residues processed: 537 average time/residue: 0.1837 time to fit residues: 165.6940 Evaluate side-chains 516 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 370 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 423 VAL Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 229 ASP Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 294 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 58 CYS Chi-restraints excluded: chain O residue 63 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 279 optimal weight: 9.9990 chunk 413 optimal weight: 50.0000 chunk 6 optimal weight: 8.9990 chunk 299 optimal weight: 20.0000 chunk 385 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 411 optimal weight: 10.0000 chunk 253 optimal weight: 20.0000 chunk 316 optimal weight: 10.0000 chunk 301 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 HIS A 369 GLN ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 HIS E 358 ASN ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 GLN G 236 GLN ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 346 HIS K 73 GLN K 168 GLN L 121 GLN L 190 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.157429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.116556 restraints weight = 44060.209| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.50 r_work: 0.2923 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 34752 Z= 0.324 Angle : 0.745 9.596 47392 Z= 0.391 Chirality : 0.052 0.226 5220 Planarity : 0.006 0.078 6120 Dihedral : 6.030 79.393 4704 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.86 % Favored : 91.11 % Rotamer: Outliers : 7.62 % Allowed : 24.25 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.12), residues: 4332 helix: -0.23 (0.26), residues: 428 sheet: -0.57 (0.15), residues: 1156 loop : -1.85 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 268 TYR 0.025 0.003 TYR A 309 PHE 0.022 0.002 PHE A 311 TRP 0.024 0.002 TRP L 188 HIS 0.009 0.002 HIS H 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00808 / 0.32 (34668) covalent geometry : angle 0.74001 / 0.39 (47224) SS BOND : bond 0.00475 / 0.33 ( 84) SS BOND : angle 1.65151 / 1.16 ( 168) hydrogen bonds : bond 0.04883 / 3.20 ( 839) hydrogen bonds : angle 6.09232 / 4.20 ( 2172) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 285 poor density : 379 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8776 (tt) REVERT: A 123 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8696 (mmtp) REVERT: A 424 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7556 (tt) REVERT: B 151 ASN cc_start: 0.9261 (OUTLIER) cc_final: 0.9042 (p0) REVERT: C 259 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6686 (tp30) REVERT: D 19 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8457 (t) REVERT: D 35 ASN cc_start: 0.8499 (m110) cc_final: 0.8231 (m-40) REVERT: D 99 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7863 (tm-30) REVERT: D 103 MET cc_start: 0.8658 (tpp) cc_final: 0.8444 (tpt) REVERT: D 226 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8221 (pt0) REVERT: D 265 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7638 (tp30) REVERT: D 309 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.6952 (m-80) REVERT: D 368 LEU cc_start: 0.8570 (pt) cc_final: 0.8144 (pt) REVERT: D 382 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8134 (mmmt) REVERT: D 422 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7383 (mm) REVERT: D 439 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.6923 (m170) REVERT: E 177 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8142 (pp) REVERT: E 221 LYS cc_start: 0.8729 (mptt) cc_final: 0.7979 (mtmt) REVERT: E 300 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8249 (p0) REVERT: E 305 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8639 (ttt-90) REVERT: E 362 LEU cc_start: 0.5673 (OUTLIER) cc_final: 0.5419 (pt) REVERT: F 236 ARG cc_start: 0.2946 (OUTLIER) cc_final: 0.2319 (mtm180) REVERT: G 44 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.8946 (tp) REVERT: G 125 HIS cc_start: 0.5711 (OUTLIER) cc_final: 0.3438 (t-170) REVERT: G 299 ASP cc_start: 0.7571 (m-30) cc_final: 0.7246 (t0) REVERT: G 397 GLU cc_start: 0.8523 (tp30) cc_final: 0.8313 (tt0) REVERT: H 205 ARG cc_start: 0.7396 (mtp85) cc_final: 0.7031 (mtm-85) REVERT: H 292 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8943 (tp) REVERT: I 185 PHE cc_start: 0.5572 (OUTLIER) cc_final: 0.5224 (m-10) REVERT: K 177 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7325 (pp) REVERT: K 229 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7164 (t0) REVERT: K 376 MET cc_start: 0.7905 (ttm) cc_final: 0.7365 (mmp) REVERT: L 211 ASP cc_start: 0.8718 (m-30) cc_final: 0.8512 (m-30) REVERT: M 53 ASP cc_start: 0.7584 (p0) cc_final: 0.7376 (p0) outliers start: 285 outliers final: 198 residues processed: 615 average time/residue: 0.1802 time to fit residues: 187.0255 Evaluate side-chains 581 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 361 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 292 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 423 VAL Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 73 GLN Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 229 ASP Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 294 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 364 THR Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 58 CYS Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 108 CYS Chi-restraints excluded: chain P residue 63 ASP Chi-restraints excluded: chain P residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 360 optimal weight: 0.7980 chunk 88 optimal weight: 30.0000 chunk 136 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 408 optimal weight: 0.3980 chunk 278 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 413 optimal weight: 20.0000 chunk 383 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 369 GLN H 155 HIS L 190 HIS O 83 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.161092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.120558 restraints weight = 43815.127| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.43 r_work: 0.2944 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34752 Z= 0.168 Angle : 0.613 8.372 47392 Z= 0.321 Chirality : 0.046 0.213 5220 Planarity : 0.005 0.068 6120 Dihedral : 5.654 80.395 4704 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 6.50 % Allowed : 25.37 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.12), residues: 4332 helix: 0.06 (0.26), residues: 428 sheet: -0.55 (0.16), residues: 1156 loop : -1.77 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 390 TYR 0.017 0.001 TYR G 137 PHE 0.012 0.001 PHE J 353 TRP 0.021 0.001 TRP L 188 HIS 0.005 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (34668) covalent geometry : angle 0.60767 / 0.32 (47224) SS BOND : bond 0.00303 / 0.20 ( 84) SS BOND : angle 1.44485 / 0.96 ( 168) hydrogen bonds : bond 0.03948 / 2.60 ( 839) hydrogen bonds : angle 5.73451 / 3.96 ( 2172) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 389 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8226 (pttt) REVERT: A 123 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8704 (mmtp) REVERT: A 362 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8602 (mt) REVERT: A 424 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7648 (tt) REVERT: B 31 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8108 (tt) REVERT: B 305 ARG cc_start: 0.9303 (OUTLIER) cc_final: 0.8808 (ttm170) REVERT: C 259 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6547 (tp30) REVERT: D 35 ASN cc_start: 0.8584 (m110) cc_final: 0.8354 (m-40) REVERT: D 99 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7964 (tm-30) REVERT: D 226 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: D 265 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7734 (tp30) REVERT: D 309 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: D 368 LEU cc_start: 0.8630 (pt) cc_final: 0.8188 (pt) REVERT: D 382 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8178 (mmmt) REVERT: D 422 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7395 (mm) REVERT: D 439 HIS cc_start: 0.7182 (OUTLIER) cc_final: 0.6234 (m170) REVERT: E 177 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7981 (pp) REVERT: E 221 LYS cc_start: 0.8634 (mptt) cc_final: 0.7915 (mtmt) REVERT: E 305 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8660 (ttt-90) REVERT: E 376 MET cc_start: 0.7148 (tpt) cc_final: 0.6765 (tpt) REVERT: F 236 ARG cc_start: 0.2567 (OUTLIER) cc_final: 0.1932 (mtm180) REVERT: G 44 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8943 (tp) REVERT: G 130 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8302 (pt0) REVERT: G 164 ILE cc_start: 0.9022 (mm) cc_final: 0.8693 (mm) REVERT: G 268 ARG cc_start: 0.9468 (OUTLIER) cc_final: 0.8131 (ptp-170) REVERT: G 299 ASP cc_start: 0.7430 (m-30) cc_final: 0.7112 (t0) REVERT: G 353 PHE cc_start: 0.7673 (p90) cc_final: 0.7301 (p90) REVERT: G 397 GLU cc_start: 0.8716 (tp30) cc_final: 0.8445 (tt0) REVERT: H 205 ARG cc_start: 0.7496 (mtp85) cc_final: 0.7074 (mtm-85) REVERT: H 284 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9232 (mt) REVERT: H 292 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8954 (tp) REVERT: I 185 PHE cc_start: 0.5753 (OUTLIER) cc_final: 0.5363 (m-10) REVERT: J 99 GLU cc_start: 0.8140 (pp20) cc_final: 0.7807 (pp20) REVERT: J 125 HIS cc_start: 0.5673 (OUTLIER) cc_final: 0.4521 (t-90) REVERT: K 114 HIS cc_start: 0.8224 (OUTLIER) cc_final: 0.7215 (m90) REVERT: K 177 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7001 (pp) REVERT: K 376 MET cc_start: 0.7947 (ttm) cc_final: 0.7364 (mmp) REVERT: L 200 PHE cc_start: 0.5511 (t80) cc_final: 0.5229 (t80) REVERT: M 53 ASP cc_start: 0.7586 (p0) cc_final: 0.7368 (p0) outliers start: 243 outliers final: 172 residues processed: 579 average time/residue: 0.1790 time to fit residues: 173.4943 Evaluate side-chains 574 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 378 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 268 ARG Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 292 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 54 LYS Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 423 VAL Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 294 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 190 HIS Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 108 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 411 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 421 optimal weight: 20.0000 chunk 345 optimal weight: 8.9990 chunk 304 optimal weight: 9.9990 chunk 247 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 295 optimal weight: 10.0000 chunk 249 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 382 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 HIS ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 369 GLN H 155 HIS J 176 ASN L 190 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.160640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.119660 restraints weight = 43698.634| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.33 r_work: 0.2937 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 34752 Z= 0.207 Angle : 0.636 8.187 47392 Z= 0.332 Chirality : 0.047 0.223 5220 Planarity : 0.005 0.068 6120 Dihedral : 5.701 81.862 4704 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.33 % Favored : 91.64 % Rotamer: Outliers : 7.06 % Allowed : 25.03 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.12), residues: 4332 helix: 0.17 (0.26), residues: 428 sheet: -0.60 (0.16), residues: 1108 loop : -1.78 (0.11), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 143 TYR 0.018 0.002 TYR A 309 PHE 0.011 0.002 PHE B 113 TRP 0.018 0.001 TRP L 188 HIS 0.011 0.001 HIS L 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 (34668) covalent geometry : angle 0.63137 / 0.33 (47224) SS BOND : bond 0.00324 / 0.22 ( 84) SS BOND : angle 1.42314 / 0.96 ( 168) hydrogen bonds : bond 0.04017 / 2.63 ( 839) hydrogen bonds : angle 5.71215 / 3.94 ( 2172) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 383 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8809 (tt) REVERT: A 54 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8233 (pttt) REVERT: A 123 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8670 (mmtp) REVERT: A 362 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8531 (mt) REVERT: A 424 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7658 (tt) REVERT: B 305 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.8829 (ttm170) REVERT: C 147 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6617 (pp30) REVERT: D 19 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8560 (t) REVERT: D 35 ASN cc_start: 0.8622 (m110) cc_final: 0.8415 (m-40) REVERT: D 99 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7960 (tm-30) REVERT: D 226 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8168 (pt0) REVERT: D 265 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7813 (tp30) REVERT: D 309 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.7339 (m-80) REVERT: D 368 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8188 (pt) REVERT: D 382 LYS cc_start: 0.8466 (mmmt) cc_final: 0.8155 (mmmt) REVERT: D 422 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7413 (mm) REVERT: D 439 HIS cc_start: 0.7139 (OUTLIER) cc_final: 0.6260 (m170) REVERT: E 157 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7192 (ptp90) REVERT: E 177 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8027 (pp) REVERT: E 221 LYS cc_start: 0.8659 (mptt) cc_final: 0.7945 (mtmt) REVERT: E 305 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8655 (ttt-90) REVERT: F 236 ARG cc_start: 0.2770 (OUTLIER) cc_final: 0.2095 (mtm180) REVERT: G 44 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9016 (tp) REVERT: G 125 HIS cc_start: 0.5620 (OUTLIER) cc_final: 0.4213 (t-170) REVERT: G 130 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8316 (pt0) REVERT: G 143 ARG cc_start: 0.7070 (ptt180) cc_final: 0.6857 (ptt90) REVERT: G 152 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6285 (mp0) REVERT: G 164 ILE cc_start: 0.9025 (mm) cc_final: 0.8705 (mm) REVERT: G 268 ARG cc_start: 0.9466 (OUTLIER) cc_final: 0.8156 (ptp-170) REVERT: G 299 ASP cc_start: 0.7462 (m-30) cc_final: 0.7141 (t0) REVERT: G 353 PHE cc_start: 0.7623 (p90) cc_final: 0.7397 (p90) REVERT: G 397 GLU cc_start: 0.8703 (tp30) cc_final: 0.8432 (tt0) REVERT: H 205 ARG cc_start: 0.7510 (mtp85) cc_final: 0.7017 (mtm-85) REVERT: H 284 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9232 (mt) REVERT: H 292 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8958 (tp) REVERT: I 185 PHE cc_start: 0.5839 (OUTLIER) cc_final: 0.5438 (m-10) REVERT: J 99 GLU cc_start: 0.7922 (pp20) cc_final: 0.7532 (pp20) REVERT: J 125 HIS cc_start: 0.5724 (OUTLIER) cc_final: 0.4628 (t-90) REVERT: K 177 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7181 (pp) REVERT: K 376 MET cc_start: 0.7944 (ttm) cc_final: 0.7357 (mmp) REVERT: L 200 PHE cc_start: 0.5663 (t80) cc_final: 0.5354 (t80) REVERT: M 53 ASP cc_start: 0.7687 (p0) cc_final: 0.7456 (p0) outliers start: 264 outliers final: 210 residues processed: 590 average time/residue: 0.1820 time to fit residues: 180.6959 Evaluate side-chains 615 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 377 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 268 ARG Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 292 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 253 ASN Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 423 VAL Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 294 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 108 CYS Chi-restraints excluded: chain P residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 373 optimal weight: 5.9990 chunk 263 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 424 optimal weight: 0.8980 chunk 232 optimal weight: 9.9990 chunk 229 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 86 optimal weight: 0.4980 chunk 129 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 HIS ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 369 GLN H 155 HIS J 176 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.161693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.120917 restraints weight = 43860.832| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.37 r_work: 0.2999 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34752 Z= 0.151 Angle : 0.594 7.846 47392 Z= 0.310 Chirality : 0.046 0.222 5220 Planarity : 0.005 0.086 6120 Dihedral : 5.517 81.952 4704 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 6.93 % Allowed : 25.29 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.12), residues: 4332 helix: 0.30 (0.27), residues: 428 sheet: -0.55 (0.16), residues: 1108 loop : -1.73 (0.11), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 143 TYR 0.016 0.001 TYR G 137 PHE 0.011 0.001 PHE J 353 TRP 0.019 0.001 TRP L 188 HIS 0.007 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (34668) covalent geometry : angle 0.58971 / 0.31 (47224) SS BOND : bond 0.00278 / 0.19 ( 84) SS BOND : angle 1.27728 / 0.91 ( 168) hydrogen bonds : bond 0.03681 / 2.42 ( 839) hydrogen bonds : angle 5.53595 / 3.81 ( 2172) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 259 poor density : 386 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8781 (tt) REVERT: A 54 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8253 (ptmt) REVERT: A 55 VAL cc_start: 0.9457 (OUTLIER) cc_final: 0.9219 (m) REVERT: A 123 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8688 (mmtp) REVERT: A 362 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8574 (mt) REVERT: B 31 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8129 (tt) REVERT: B 305 ARG cc_start: 0.9293 (OUTLIER) cc_final: 0.8822 (ttm170) REVERT: C 147 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6541 (pp30) REVERT: D 19 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8597 (t) REVERT: D 35 ASN cc_start: 0.8649 (m110) cc_final: 0.8448 (m-40) REVERT: D 99 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8058 (tm-30) REVERT: D 226 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8038 (pt0) REVERT: D 265 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7822 (tp30) REVERT: D 301 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8018 (tp30) REVERT: D 306 GLU cc_start: 0.7709 (tp30) cc_final: 0.7297 (tt0) REVERT: D 309 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7378 (m-80) REVERT: D 368 LEU cc_start: 0.8663 (pt) cc_final: 0.8228 (pt) REVERT: D 382 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8145 (mmmt) REVERT: D 439 HIS cc_start: 0.7140 (OUTLIER) cc_final: 0.6236 (m170) REVERT: E 177 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8191 (pp) REVERT: E 221 LYS cc_start: 0.8773 (mptt) cc_final: 0.8068 (mtmt) REVERT: E 305 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8635 (ttt-90) REVERT: G 44 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9016 (tp) REVERT: G 130 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8360 (pt0) REVERT: G 152 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6337 (mp0) REVERT: G 164 ILE cc_start: 0.9029 (mm) cc_final: 0.8720 (mm) REVERT: G 268 ARG cc_start: 0.9447 (OUTLIER) cc_final: 0.7941 (ptp-170) REVERT: G 299 ASP cc_start: 0.7498 (m-30) cc_final: 0.7183 (t0) REVERT: G 353 PHE cc_start: 0.7613 (p90) cc_final: 0.7394 (p90) REVERT: G 397 GLU cc_start: 0.8692 (tp30) cc_final: 0.8420 (tt0) REVERT: H 205 ARG cc_start: 0.7487 (mtp85) cc_final: 0.7026 (mtm-85) REVERT: H 284 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9243 (mt) REVERT: H 292 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8964 (tp) REVERT: I 185 PHE cc_start: 0.5804 (OUTLIER) cc_final: 0.5384 (m-10) REVERT: J 99 GLU cc_start: 0.7848 (pp20) cc_final: 0.7533 (pp20) REVERT: J 125 HIS cc_start: 0.5466 (OUTLIER) cc_final: 0.4427 (t-90) REVERT: K 114 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7216 (m90) REVERT: K 177 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7097 (pp) REVERT: K 376 MET cc_start: 0.8013 (ttm) cc_final: 0.7429 (mmp) REVERT: M 53 ASP cc_start: 0.7706 (p0) cc_final: 0.7491 (p0) outliers start: 259 outliers final: 206 residues processed: 589 average time/residue: 0.1783 time to fit residues: 175.5304 Evaluate side-chains 610 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 378 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 268 ARG Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 292 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 253 ASN Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 309 TYR Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 423 VAL Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 294 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 67 CYS Chi-restraints excluded: chain O residue 108 CYS Chi-restraints excluded: chain P residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 403 optimal weight: 8.9990 chunk 389 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 422 optimal weight: 3.9990 chunk 166 optimal weight: 50.0000 chunk 24 optimal weight: 2.9990 chunk 266 optimal weight: 20.0000 chunk 353 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 369 GLN H 155 HIS J 100 ASN J 176 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.161448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.120407 restraints weight = 43589.865| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.30 r_work: 0.2993 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34752 Z= 0.167 Angle : 0.605 10.287 47392 Z= 0.316 Chirality : 0.046 0.239 5220 Planarity : 0.005 0.077 6120 Dihedral : 5.526 81.738 4704 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 7.25 % Allowed : 24.97 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.71 (0.12), residues: 4332 helix: 0.37 (0.27), residues: 428 sheet: -0.55 (0.16), residues: 1120 loop : -1.72 (0.11), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 143 TYR 0.015 0.001 TYR G 137 PHE 0.011 0.001 PHE J 355 TRP 0.020 0.001 TRP L 188 HIS 0.005 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (34668) covalent geometry : angle 0.59960 / 0.31 (47224) SS BOND : bond 0.00300 / 0.20 ( 84) SS BOND : angle 1.51790 / 1.03 ( 168) hydrogen bonds : bond 0.03692 / 2.43 ( 839) hydrogen bonds : angle 5.53219 / 3.82 ( 2172) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 271 poor density : 387 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8795 (tt) REVERT: A 54 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8223 (ptmt) REVERT: A 55 VAL cc_start: 0.9463 (OUTLIER) cc_final: 0.9225 (m) REVERT: A 95 PHE cc_start: 0.7895 (t80) cc_final: 0.7567 (t80) REVERT: A 123 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8676 (mmtp) REVERT: A 362 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8549 (mt) REVERT: B 305 ARG cc_start: 0.9300 (OUTLIER) cc_final: 0.8833 (ttm170) REVERT: C 147 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6552 (pp30) REVERT: D 19 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8583 (t) REVERT: D 99 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7940 (tm-30) REVERT: D 226 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8025 (pt0) REVERT: D 265 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7785 (tp30) REVERT: D 301 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: D 309 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7335 (m-80) REVERT: D 349 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: D 368 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8214 (pt) REVERT: D 382 LYS cc_start: 0.8478 (mmmt) cc_final: 0.8136 (mmmt) REVERT: D 439 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6324 (m170) REVERT: E 157 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7353 (ptp90) REVERT: E 177 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8193 (pp) REVERT: E 305 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8633 (ttt-90) REVERT: E 362 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5782 (pt) REVERT: F 236 ARG cc_start: 0.2801 (OUTLIER) cc_final: 0.2131 (mtm180) REVERT: G 44 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9012 (tp) REVERT: G 130 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8328 (pt0) REVERT: G 152 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6348 (mp0) REVERT: G 164 ILE cc_start: 0.9023 (mm) cc_final: 0.8717 (mm) REVERT: G 268 ARG cc_start: 0.9425 (OUTLIER) cc_final: 0.8117 (ptp-170) REVERT: G 299 ASP cc_start: 0.7500 (m-30) cc_final: 0.7192 (t0) REVERT: G 397 GLU cc_start: 0.8668 (tp30) cc_final: 0.8405 (tt0) REVERT: H 205 ARG cc_start: 0.7416 (mtp85) cc_final: 0.7072 (mtm-85) REVERT: H 284 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9230 (mt) REVERT: H 292 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8975 (tp) REVERT: I 185 PHE cc_start: 0.5785 (OUTLIER) cc_final: 0.5416 (m-10) REVERT: J 99 GLU cc_start: 0.7824 (pp20) cc_final: 0.7463 (pp20) REVERT: J 125 HIS cc_start: 0.5486 (OUTLIER) cc_final: 0.4520 (t-90) REVERT: K 114 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7172 (m90) REVERT: K 177 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7111 (pp) REVERT: K 200 LYS cc_start: 0.7784 (tppp) cc_final: 0.7210 (tptt) REVERT: K 376 MET cc_start: 0.7991 (ttm) cc_final: 0.7420 (mmp) REVERT: L 200 PHE cc_start: 0.5320 (t80) cc_final: 0.4987 (t80) REVERT: M 53 ASP cc_start: 0.7766 (p0) cc_final: 0.7542 (p0) outliers start: 271 outliers final: 224 residues processed: 598 average time/residue: 0.1878 time to fit residues: 187.4790 Evaluate side-chains 638 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 384 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 268 ARG Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 292 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 253 ASN Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 309 TYR Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 423 VAL Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 233 TRP Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 294 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 67 CYS Chi-restraints excluded: chain O residue 108 CYS Chi-restraints excluded: chain P residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 253 optimal weight: 20.0000 chunk 195 optimal weight: 20.0000 chunk 296 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 350 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 175 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 386 optimal weight: 2.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN B 151 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS E 222 GLN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS J 176 ASN K 73 GLN K 168 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.157314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.116581 restraints weight = 43889.896| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.42 r_work: 0.2928 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 34752 Z= 0.282 Angle : 0.708 13.506 47392 Z= 0.370 Chirality : 0.050 0.259 5220 Planarity : 0.006 0.077 6120 Dihedral : 5.978 82.691 4704 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.98 % Favored : 91.00 % Rotamer: Outliers : 7.43 % Allowed : 24.89 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.93 (0.12), residues: 4332 helix: 0.21 (0.26), residues: 428 sheet: -0.72 (0.16), residues: 1068 loop : -1.85 (0.11), residues: 2836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 143 TYR 0.020 0.002 TYR A 309 PHE 0.039 0.002 PHE G 353 TRP 0.024 0.002 TRP L 188 HIS 0.008 0.001 HIS J 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.28 (34668) covalent geometry : angle 0.70072 / 0.37 (47224) SS BOND : bond 0.00411 / 0.28 ( 84) SS BOND : angle 1.88344 / 1.26 ( 168) hydrogen bonds : bond 0.04340 / 2.84 ( 839) hydrogen bonds : angle 5.80130 / 4.01 ( 2172) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 278 poor density : 387 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8822 (tt) REVERT: A 54 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8351 (pttt) REVERT: A 123 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8763 (mmtp) REVERT: A 362 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8604 (mt) REVERT: B 151 ASN cc_start: 0.9345 (OUTLIER) cc_final: 0.9032 (p0) REVERT: B 305 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.8813 (ttm170) REVERT: C 147 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6499 (pp30) REVERT: C 259 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7048 (pm20) REVERT: D 19 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8629 (t) REVERT: D 99 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7935 (tm-30) REVERT: D 226 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8239 (pt0) REVERT: D 265 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7972 (tp30) REVERT: D 301 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8130 (tp30) REVERT: D 309 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: D 344 ASP cc_start: 0.8655 (p0) cc_final: 0.8389 (p0) REVERT: D 349 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7637 (mm-30) REVERT: D 368 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8138 (pt) REVERT: D 382 LYS cc_start: 0.8490 (mmmt) cc_final: 0.8158 (mmmt) REVERT: D 439 HIS cc_start: 0.7238 (OUTLIER) cc_final: 0.6474 (m170) REVERT: E 35 GLU cc_start: 0.8030 (tp30) cc_final: 0.7770 (tm-30) REVERT: E 157 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7342 (ptp90) REVERT: E 177 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8249 (pp) REVERT: E 221 LYS cc_start: 0.8844 (mptt) cc_final: 0.8060 (mtmt) REVERT: E 305 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8717 (ttt-90) REVERT: E 362 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5891 (pt) REVERT: F 236 ARG cc_start: 0.2879 (OUTLIER) cc_final: 0.2169 (mtm180) REVERT: G 44 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9020 (tp) REVERT: G 125 HIS cc_start: 0.6074 (OUTLIER) cc_final: 0.4535 (t-170) REVERT: G 130 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8434 (pt0) REVERT: G 152 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: G 164 ILE cc_start: 0.9043 (mm) cc_final: 0.8754 (mm) REVERT: G 268 ARG cc_start: 0.9502 (OUTLIER) cc_final: 0.8366 (ptp-170) REVERT: G 299 ASP cc_start: 0.7489 (m-30) cc_final: 0.7161 (t0) REVERT: G 353 PHE cc_start: 0.7668 (p90) cc_final: 0.7118 (p90) REVERT: G 397 GLU cc_start: 0.8700 (tp30) cc_final: 0.8432 (tt0) REVERT: H 284 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9224 (mt) REVERT: H 292 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8999 (tp) REVERT: H 379 CYS cc_start: 0.6363 (t) cc_final: 0.5249 (p) REVERT: I 176 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7639 (pp30) REVERT: I 185 PHE cc_start: 0.5864 (OUTLIER) cc_final: 0.5489 (m-10) REVERT: J 99 GLU cc_start: 0.8097 (pp20) cc_final: 0.7697 (pp20) REVERT: J 125 HIS cc_start: 0.5724 (OUTLIER) cc_final: 0.4514 (t-90) REVERT: K 114 HIS cc_start: 0.8374 (OUTLIER) cc_final: 0.7401 (m90) REVERT: K 177 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7305 (pp) REVERT: K 194 GLN cc_start: 0.8228 (mt0) cc_final: 0.7922 (mp10) REVERT: K 200 LYS cc_start: 0.7940 (tppp) cc_final: 0.7288 (tptt) REVERT: K 376 MET cc_start: 0.7980 (ttm) cc_final: 0.7415 (mmp) REVERT: L 171 LYS cc_start: 0.5740 (OUTLIER) cc_final: 0.5378 (pttm) REVERT: L 200 PHE cc_start: 0.5402 (t80) cc_final: 0.5037 (t80) REVERT: M 53 ASP cc_start: 0.7785 (p0) cc_final: 0.7485 (p0) outliers start: 278 outliers final: 225 residues processed: 606 average time/residue: 0.1748 time to fit residues: 177.8938 Evaluate side-chains 634 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 259 poor density : 375 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 268 ARG Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 292 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 253 ASN Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 309 TYR Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 423 VAL Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 73 GLN Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 233 TRP Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 294 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 67 CYS Chi-restraints excluded: chain O residue 108 CYS Chi-restraints excluded: chain P residue 63 ASP Chi-restraints excluded: chain P residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 24 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 396 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 94 optimal weight: 30.0000 chunk 40 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS J 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.160302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.119339 restraints weight = 43788.744| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.28 r_work: 0.2949 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 34752 Z= 0.189 Angle : 0.640 11.602 47392 Z= 0.336 Chirality : 0.047 0.260 5220 Planarity : 0.005 0.072 6120 Dihedral : 5.838 82.863 4704 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 6.84 % Allowed : 25.40 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.12), residues: 4332 helix: 0.29 (0.27), residues: 428 sheet: -0.66 (0.16), residues: 1080 loop : -1.80 (0.11), residues: 2824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 143 TYR 0.015 0.002 TYR G 137 PHE 0.036 0.002 PHE G 353 TRP 0.022 0.001 TRP L 188 HIS 0.006 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 (34668) covalent geometry : angle 0.63254 / 0.33 (47224) SS BOND : bond 0.00349 / 0.24 ( 84) SS BOND : angle 1.77662 / 1.17 ( 168) hydrogen bonds : bond 0.03885 / 2.55 ( 839) hydrogen bonds : angle 5.63201 / 3.88 ( 2172) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 381 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8822 (tt) REVERT: A 54 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8243 (ptmt) REVERT: A 123 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8684 (mmtp) REVERT: A 362 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8559 (mt) REVERT: B 151 ASN cc_start: 0.9265 (OUTLIER) cc_final: 0.9060 (p0) REVERT: B 305 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8810 (ttm170) REVERT: C 147 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6566 (pp30) REVERT: C 259 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: D 19 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8601 (t) REVERT: D 99 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7851 (tm-30) REVERT: D 226 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8075 (pt0) REVERT: D 301 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8011 (tp30) REVERT: D 309 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7172 (m-80) REVERT: D 344 ASP cc_start: 0.8547 (p0) cc_final: 0.8274 (p0) REVERT: D 349 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7638 (mm-30) REVERT: D 368 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8125 (pt) REVERT: D 382 LYS cc_start: 0.8487 (mmmt) cc_final: 0.8147 (mmmt) REVERT: D 439 HIS cc_start: 0.7192 (OUTLIER) cc_final: 0.6487 (m170) REVERT: E 58 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6599 (p0) REVERT: E 157 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7403 (ptp90) REVERT: E 177 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8194 (pp) REVERT: E 305 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8632 (ttt-90) REVERT: E 362 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5839 (pt) REVERT: G 44 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9013 (tp) REVERT: G 125 HIS cc_start: 0.5735 (OUTLIER) cc_final: 0.4302 (t-170) REVERT: G 130 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8356 (pt0) REVERT: G 152 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6452 (mp0) REVERT: G 164 ILE cc_start: 0.9010 (mm) cc_final: 0.8711 (mm) REVERT: G 268 ARG cc_start: 0.9468 (OUTLIER) cc_final: 0.8184 (ptp-170) REVERT: G 299 ASP cc_start: 0.7485 (m-30) cc_final: 0.7186 (t0) REVERT: G 353 PHE cc_start: 0.7474 (p90) cc_final: 0.6995 (p90) REVERT: G 397 GLU cc_start: 0.8672 (tp30) cc_final: 0.8409 (tt0) REVERT: H 284 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9242 (mt) REVERT: H 292 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8973 (tp) REVERT: H 379 CYS cc_start: 0.6235 (t) cc_final: 0.5062 (p) REVERT: I 185 PHE cc_start: 0.5858 (OUTLIER) cc_final: 0.5464 (m-10) REVERT: J 99 GLU cc_start: 0.7891 (pp20) cc_final: 0.7485 (pp20) REVERT: J 125 HIS cc_start: 0.5483 (OUTLIER) cc_final: 0.4365 (t-90) REVERT: K 114 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.7314 (m90) REVERT: K 177 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7279 (pp) REVERT: K 194 GLN cc_start: 0.8128 (mt0) cc_final: 0.7886 (mp10) REVERT: K 200 LYS cc_start: 0.7696 (tppp) cc_final: 0.7206 (tptt) REVERT: K 376 MET cc_start: 0.7979 (ttm) cc_final: 0.7410 (mmp) REVERT: L 200 PHE cc_start: 0.5373 (t80) cc_final: 0.5010 (t80) REVERT: M 53 ASP cc_start: 0.7751 (p0) cc_final: 0.7453 (p0) REVERT: O 110 MET cc_start: 0.2429 (mmt) cc_final: 0.2203 (mmt) outliers start: 256 outliers final: 218 residues processed: 583 average time/residue: 0.1785 time to fit residues: 174.5375 Evaluate side-chains 625 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 376 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 268 ARG Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 292 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 253 ASN Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 309 TYR Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 423 VAL Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 233 TRP Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 294 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 67 CYS Chi-restraints excluded: chain O residue 108 CYS Chi-restraints excluded: chain P residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 316 optimal weight: 2.9990 chunk 420 optimal weight: 0.0670 chunk 17 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 231 optimal weight: 0.0170 chunk 366 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 352 optimal weight: 10.0000 chunk 259 optimal weight: 0.9980 chunk 406 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 176 GLN E 222 GLN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 HIS G 369 GLN H 155 HIS H 230 ASN J 30 GLN K 329 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.167758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.132489 restraints weight = 43280.285| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.55 r_work: 0.2953 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 34752 Z= 0.100 Angle : 0.556 8.271 47392 Z= 0.291 Chirality : 0.044 0.276 5220 Planarity : 0.005 0.059 6120 Dihedral : 5.205 80.994 4704 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.77 % Allowed : 28.48 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.12), residues: 4332 helix: 0.66 (0.27), residues: 420 sheet: -0.46 (0.16), residues: 1092 loop : -1.64 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 143 TYR 0.015 0.001 TYR G 137 PHE 0.030 0.001 PHE G 353 TRP 0.023 0.001 TRP I 188 HIS 0.007 0.001 HIS G 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (34668) covalent geometry : angle 0.55136 / 0.29 (47224) SS BOND : bond 0.00250 / 0.17 ( 84) SS BOND : angle 1.36800 / 0.95 ( 168) hydrogen bonds : bond 0.03055 / 2.03 ( 839) hydrogen bonds : angle 5.22135 / 3.60 ( 2172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9241.91 seconds wall clock time: 158 minutes 25.76 seconds (9505.76 seconds total)