Starting phenix.real_space_refine on Mon Oct 13 11:55:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xi5_38371/10_2025/8xi5_38371_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xi5_38371/10_2025/8xi5_38371.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xi5_38371/10_2025/8xi5_38371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xi5_38371/10_2025/8xi5_38371.map" model { file = "/net/cci-nas-00/data/ceres_data/8xi5_38371/10_2025/8xi5_38371_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xi5_38371/10_2025/8xi5_38371_neut.cif" } 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= 0.009 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 240 5.16 5 C 21316 2.51 5 N 5900 2.21 5 O 6356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 233 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33820 Number of models: 1 Model: "" Number of chains: 28 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: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "N" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "O" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "P" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "Q" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 310 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "R" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 310 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "S" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 310 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "T" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 310 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.20, per 1000 atoms: 0.27 Number of scatterers: 33820 At special positions: 0 Unit cell: (183.54, 200.83, 207.48, 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 240 16.00 O 6356 8.00 N 5900 7.00 C 21316 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=2.03 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=2.03 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=2.02 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=2.02 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=2.03 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=2.02 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=2.01 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=2.03 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=2.01 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=1.95 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 217 " distance=2.02 Simple disulfide: pdb=" SG CYS H 393 " - pdb=" SG CYS H 414 " distance=2.04 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=2.04 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=2.02 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS K 393 " - pdb=" SG CYS K 414 " distance=2.04 Simple disulfide: pdb=" SG CYS M 193 " - pdb=" SG CYS M 205 " distance=2.04 Simple disulfide: pdb=" SG CYS M 200 " - pdb=" SG CYS M 218 " distance=2.03 Simple disulfide: pdb=" SG CYS M 212 " - pdb=" SG CYS M 229 " distance=2.03 Simple disulfide: pdb=" SG CYS N 193 " - pdb=" SG CYS N 205 " distance=2.03 Simple disulfide: pdb=" SG CYS N 200 " - pdb=" SG CYS N 218 " distance=2.03 Simple disulfide: pdb=" SG CYS N 212 " - pdb=" SG CYS N 229 " distance=2.03 Simple disulfide: pdb=" SG CYS O 193 " - pdb=" SG CYS O 205 " distance=2.03 Simple disulfide: pdb=" SG CYS O 200 " - pdb=" SG CYS O 218 " distance=2.03 Simple disulfide: pdb=" SG CYS O 212 " - pdb=" SG CYS O 229 " distance=2.03 Simple disulfide: pdb=" SG CYS P 193 " - pdb=" SG CYS P 205 " distance=2.03 Simple disulfide: pdb=" SG CYS P 200 " - pdb=" SG CYS P 218 " distance=2.03 Simple disulfide: pdb=" SG CYS P 212 " - pdb=" SG CYS P 229 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 113 " - pdb=" SG CYS Q 127 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 120 " - pdb=" SG CYS Q 140 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 134 " - pdb=" SG CYS Q 149 " distance=1.89 Simple disulfide: pdb=" SG CYS R 113 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 120 " - pdb=" SG CYS R 140 " distance=2.03 Simple disulfide: pdb=" SG CYS R 134 " - pdb=" SG CYS R 149 " distance=2.44 Simple disulfide: pdb=" SG CYS S 113 " - pdb=" SG CYS S 127 " distance=2.03 Simple disulfide: pdb=" SG CYS S 120 " - pdb=" SG CYS S 140 " distance=2.03 Simple disulfide: pdb=" SG CYS S 134 " - pdb=" SG CYS S 149 " distance=2.03 Simple disulfide: pdb=" SG CYS T 113 " - pdb=" SG CYS T 127 " distance=2.03 Simple disulfide: pdb=" SG CYS T 120 " - pdb=" SG CYS T 140 " distance=2.03 Simple disulfide: pdb=" SG CYS T 134 " - pdb=" SG CYS T 149 " 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: 2.50 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8088 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 101 sheets defined 12.9% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.818A 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 256 Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.751A pdb=" N PHE A 288 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.522A pdb=" N THR A 294 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 441 removed outlier: 4.312A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.520A pdb=" N PHE B 6 " --> pdb=" O LEU B 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 6' Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.520A pdb=" N ALA B 12 " --> pdb=" O TYR B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 348 through 360 Processing helix chain 'B' and resid 365 through 395 removed outlier: 3.716A pdb=" N CYS B 369 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG B 388 " --> pdb=" O TRP B 384 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 412 removed outlier: 3.523A pdb=" N ALA B 410 " --> pdb=" O PRO B 406 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.952A pdb=" N MET C 170 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 248 removed outlier: 3.667A 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: 3.613A pdb=" N PHE D 288 " --> pdb=" O ASP D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.532A pdb=" N GLU D 293 " --> pdb=" O ARG D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 440 removed outlier: 3.575A pdb=" N THR D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 430 " --> pdb=" O LEU D 426 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 432 " --> pdb=" O ALA D 428 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 433 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 12 Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 348 through 358 removed outlier: 3.961A pdb=" N VAL E 353 " --> pdb=" O PRO E 349 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL E 354 " --> pdb=" O HIS E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 395 removed outlier: 3.550A pdb=" N ALA E 373 " --> pdb=" O CYS E 369 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS E 379 " --> pdb=" O ILE E 375 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE E 394 " --> pdb=" O ARG E 390 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR E 395 " --> pdb=" O ASN E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 removed outlier: 4.200A pdb=" N LEU E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) removed outlier: 3.525A 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 167 through 171 removed outlier: 4.066A pdb=" N MET F 170 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 4.184A pdb=" N SER G 115 " --> pdb=" O GLU G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 247 removed outlier: 3.663A pdb=" N LYS G 246 " --> pdb=" O GLU G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 255 Processing helix chain 'G' and resid 284 through 288 removed outlier: 3.646A pdb=" N ALA G 287 " --> pdb=" O PRO G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 399 through 403 removed outlier: 4.398A pdb=" N ALA G 402 " --> pdb=" O PHE G 399 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE G 403 " --> pdb=" O THR G 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 399 through 403' Processing helix chain 'G' and resid 404 through 411 Processing helix chain 'G' and resid 416 through 438 removed outlier: 3.776A pdb=" N VAL G 423 " --> pdb=" O SER G 419 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU G 424 " --> pdb=" O ALA G 420 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR G 429 " --> pdb=" O GLY G 425 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU G 434 " --> pdb=" O ALA G 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 7 removed outlier: 3.986A pdb=" N THR H 7 " --> pdb=" O THR H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 221 No H-bonds generated for 'chain 'H' and resid 219 through 221' Processing helix chain 'H' and resid 348 through 360 removed outlier: 3.571A pdb=" N VAL H 353 " --> pdb=" O PRO H 349 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL H 354 " --> pdb=" O HIS H 350 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR H 355 " --> pdb=" O GLU H 351 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR H 356 " --> pdb=" O VAL H 352 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN H 358 " --> pdb=" O VAL H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 384 removed outlier: 4.214A pdb=" N ILE H 365 " --> pdb=" O PRO H 361 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE H 366 " --> pdb=" O LEU H 362 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR H 370 " --> pdb=" O ILE H 366 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL H 380 " --> pdb=" O MET H 376 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR H 381 " --> pdb=" O VAL H 377 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER H 382 " --> pdb=" O SER H 378 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL H 383 " --> pdb=" O CYS H 379 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 399 removed outlier: 3.619A pdb=" N ILE H 394 " --> pdb=" O ARG H 390 " (cutoff:3.500A) Proline residue: H 396 - end of helix removed outlier: 3.735A pdb=" N LEU H 399 " --> pdb=" O THR H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 412 removed outlier: 4.172A pdb=" N LEU H 411 " --> pdb=" O ILE H 407 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU H 412 " --> pdb=" O LEU H 408 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 116 removed outlier: 4.052A pdb=" N SER J 115 " --> pdb=" O GLU J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 248 removed outlier: 3.661A pdb=" N LYS J 246 " --> pdb=" O GLU J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 256 removed outlier: 3.517A pdb=" N VAL J 255 " --> pdb=" O PRO J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 260 Processing helix chain 'J' and resid 284 through 288 removed outlier: 3.827A pdb=" N PHE J 288 " --> pdb=" O ASP J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 294 removed outlier: 3.529A pdb=" N THR J 294 " --> pdb=" O ILE J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 441 removed outlier: 3.518A pdb=" N LEU J 426 " --> pdb=" O ILE J 422 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU J 434 " --> pdb=" O ALA J 430 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG J 440 " --> pdb=" O LEU J 436 " (cutoff:3.500A) removed outlier: 3.551A 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 219 through 221 No H-bonds generated for 'chain 'K' and resid 219 through 221' Processing helix chain 'K' and resid 348 through 360 removed outlier: 4.197A pdb=" N VAL K 354 " --> pdb=" O HIS K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 399 removed outlier: 3.536A pdb=" N CYS K 369 " --> pdb=" O ILE K 365 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS K 371 " --> pdb=" O GLY K 367 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE K 394 " --> pdb=" O ARG K 390 " (cutoff:3.500A) Proline residue: K 396 - end of helix Processing helix chain 'L' and resid 145 through 150 removed outlier: 3.955A pdb=" N ALA L 150 " --> pdb=" O GLU L 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 209 through 211 No H-bonds generated for 'chain 'M' and resid 209 through 211' Processing helix chain 'M' and resid 221 through 225 removed outlier: 3.520A pdb=" N GLU M 224 " --> pdb=" O GLN M 221 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER M 225 " --> pdb=" O SER M 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 221 through 225' Processing helix chain 'N' and resid 209 through 211 No H-bonds generated for 'chain 'N' and resid 209 through 211' Processing helix chain 'N' and resid 225 through 230 removed outlier: 3.515A pdb=" N GLY N 230 " --> pdb=" O LEU N 226 " (cutoff:3.500A) Processing helix chain 'O' and resid 209 through 211 No H-bonds generated for 'chain 'O' and resid 209 through 211' Processing helix chain 'O' and resid 225 through 230 Processing helix chain 'P' and resid 209 through 211 No H-bonds generated for 'chain 'P' and resid 209 through 211' Processing helix chain 'P' and resid 221 through 225 removed outlier: 3.711A pdb=" N GLU P 224 " --> pdb=" O GLN P 221 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER P 225 " --> pdb=" O SER P 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 221 through 225' 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: 6.490A pdb=" N MET A 132 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR A 36 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN A 130 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE A 38 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR A 128 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR A 42 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL A 124 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TYR A 46 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 133 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 145 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TYR A 137 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N SER A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.490A pdb=" N MET A 132 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR A 36 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN A 130 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE A 38 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR A 128 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR A 42 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL A 124 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TYR A 46 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA6, first strand: chain 'A' and resid 204 through 205 Processing sheet with id=AA7, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA8, first strand: chain 'A' and resid 297 through 306 removed outlier: 6.562A pdb=" N LEU A 300 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LYS A 322 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N CYS A 302 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ALA A 320 " --> pdb=" O CYS A 302 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE A 304 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR A 318 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.683A pdb=" N VAL A 345 " --> pdb=" O CYS A 329 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS A 329 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AB2, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.524A pdb=" N ALA B 17 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 34 through 37 removed outlier: 3.558A pdb=" N GLN B 48 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL B 36 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG B 46 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N SER B 50 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N MET B 68 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B 72 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 34 through 37 removed outlier: 3.558A pdb=" N GLN B 48 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL B 36 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG B 46 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR B 97 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N ALA B 51 " --> pdb=" O HIS B 95 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N HIS B 95 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N PHE B 53 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 11.130A pdb=" N SER B 93 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL B 83 " --> pdb=" O CYS B 89 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 108 " --> pdb=" O HIS B 126 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N HIS B 126 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N THR B 110 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL B 124 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY B 112 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N CYS B 122 " --> pdb=" O GLY B 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 146 through 153 Processing sheet with id=AB6, first strand: chain 'B' and resid 163 through 164 Processing sheet with id=AB7, first strand: chain 'B' and resid 166 through 167 Processing sheet with id=AB8, first strand: chain 'B' and resid 178 through 180 Processing sheet with id=AB9, first strand: chain 'B' and resid 207 through 208 removed outlier: 3.644A pdb=" N GLY B 207 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 272 through 275 Processing sheet with id=AC2, first strand: chain 'C' and resid 132 through 133 removed outlier: 5.485A pdb=" N VAL C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 118 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY C 124 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 175 through 176 removed outlier: 6.751A pdb=" N LEU C 175 " --> pdb=" O VAL C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 186 through 188 removed outlier: 3.577A pdb=" N TRP C 188 " --> pdb=" O GLY C 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 215 through 216 removed outlier: 3.861A pdb=" N ALA C 225 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE C 226 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N SER C 240 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AC7, first strand: chain 'D' and resid 15 through 19 removed outlier: 6.703A pdb=" N LEU D 29 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TYR D 137 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE D 31 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE D 135 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 33 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL D 133 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASN D 35 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA D 131 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG D 37 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL D 129 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE D 39 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY D 127 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA D 121 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 15 through 19 removed outlier: 6.703A pdb=" N LEU D 29 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TYR D 137 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE D 31 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE D 135 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 33 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL D 133 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASN D 35 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA D 131 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG D 37 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL D 129 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE D 39 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY D 127 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA D 121 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AD1, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AD2, first strand: chain 'D' and resid 205 through 206 Processing sheet with id=AD3, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AD4, first strand: chain 'D' and resid 261 through 262 Processing sheet with id=AD5, first strand: chain 'D' and resid 297 through 306 removed outlier: 6.943A pdb=" N LEU D 300 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LYS D 322 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N CYS D 302 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA D 320 " --> pdb=" O CYS D 302 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE D 304 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR D 318 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 339 " --> pdb=" O SER D 358 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 344 through 347 removed outlier: 3.563A pdb=" N VAL D 345 " --> pdb=" O CYS D 329 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS D 329 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS D 332 " --> pdb=" O GLN D 369 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AD8, first strand: chain 'E' and resid 17 through 18 Processing sheet with id=AD9, first strand: chain 'E' and resid 34 through 37 removed outlier: 3.554A pdb=" N GLN E 48 " --> pdb=" O GLU E 34 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL E 36 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG E 46 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N SER E 50 " --> pdb=" O MET E 68 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N MET E 68 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N TYR E 64 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR E 72 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 34 through 37 removed outlier: 3.554A pdb=" N GLN E 48 " --> pdb=" O GLU E 34 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL E 36 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG E 46 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR E 97 " --> pdb=" O THR E 49 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N ALA E 51 " --> pdb=" O HIS E 95 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N HIS E 95 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N PHE E 53 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N SER E 93 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 16.503A pdb=" N LEU E 55 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 18.831A pdb=" N LEU E 91 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AE3, first strand: chain 'E' and resid 146 through 153 Processing sheet with id=AE4, first strand: chain 'E' and resid 234 through 235 Processing sheet with id=AE5, first strand: chain 'E' and resid 178 through 180 Processing sheet with id=AE6, first strand: chain 'E' and resid 207 through 208 removed outlier: 3.645A pdb=" N GLY E 207 " --> pdb=" O TYR E 197 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 272 through 276 removed outlier: 3.739A pdb=" N THR E 279 " --> pdb=" O LYS E 276 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 121 through 127 removed outlier: 5.584A pdb=" N VAL F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU F 118 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY F 124 " --> pdb=" O ILE F 116 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 186 through 187 Processing sheet with id=AF1, first strand: chain 'F' and resid 215 through 217 removed outlier: 6.538A pdb=" N ILE F 216 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N VAL F 224 " --> pdb=" O TRP F 244 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TRP F 244 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE F 226 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER F 240 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 2 through 5 removed outlier: 3.591A pdb=" N ALA G 5 " --> pdb=" O ILE G 279 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS G 161 " --> pdb=" O ASP G 282 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 15 through 19 removed outlier: 3.735A pdb=" N VAL G 27 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR G 136 " --> pdb=" O GLN G 30 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET G 132 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N THR G 36 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLN G 130 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE G 38 " --> pdb=" O THR G 128 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR G 128 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR G 126 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR G 42 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL G 124 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU G 44 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR G 122 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR G 46 " --> pdb=" O LYS G 120 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS G 120 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU G 184 " --> pdb=" O TYR G 181 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 140 through 148 removed outlier: 5.420A pdb=" N SER G 141 " --> pdb=" O TYR G 137 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TYR G 137 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL G 133 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA G 131 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS G 120 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR G 46 " --> pdb=" O LYS G 120 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR G 122 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU G 44 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL G 124 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR G 42 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR G 126 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR G 128 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE G 38 " --> pdb=" O THR G 128 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLN G 130 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N THR G 36 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET G 132 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR G 136 " --> pdb=" O GLN G 30 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AF6, first strand: chain 'G' and resid 60 through 61 removed outlier: 3.562A pdb=" N PHE G 81 " --> pdb=" O GLN G 102 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AF8, first strand: chain 'G' and resid 261 through 262 Processing sheet with id=AF9, first strand: chain 'G' and resid 297 through 307 removed outlier: 6.937A pdb=" N LEU G 300 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LYS G 322 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N CYS G 302 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA G 320 " --> pdb=" O CYS G 302 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE G 304 " --> pdb=" O THR G 318 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR G 318 " --> pdb=" O ILE G 304 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL G 339 " --> pdb=" O SER G 358 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 331 through 332 Processing sheet with id=AG2, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AG3, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=AG4, first strand: chain 'H' and resid 34 through 37 removed outlier: 3.713A pdb=" N GLN H 48 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL H 36 " --> pdb=" O ARG H 46 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG H 46 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 10.235A pdb=" N SER H 50 " --> pdb=" O MET H 68 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N MET H 68 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE H 67 " --> pdb=" O LYS H 74 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN H 69 " --> pdb=" O THR H 72 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 34 through 37 removed outlier: 3.713A pdb=" N GLN H 48 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL H 36 " --> pdb=" O ARG H 46 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG H 46 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N TYR H 97 " --> pdb=" O THR H 49 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N ALA H 51 " --> pdb=" O HIS H 95 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N HIS H 95 " --> pdb=" O ALA H 51 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N PHE H 53 " --> pdb=" O SER H 93 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N SER H 93 " --> pdb=" O PHE H 53 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 81 through 84 removed outlier: 4.984A pdb=" N ASP H 107 " --> pdb=" O HIS H 126 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N HIS H 126 " --> pdb=" O ASP H 107 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 146 through 153 Processing sheet with id=AG8, first strand: chain 'H' and resid 234 through 235 Processing sheet with id=AG9, first strand: chain 'H' and resid 178 through 180 Processing sheet with id=AH1, first strand: chain 'H' and resid 207 through 208 Processing sheet with id=AH2, first strand: chain 'H' and resid 272 through 276 removed outlier: 3.614A pdb=" N THR H 279 " --> pdb=" O LYS H 276 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 121 through 125 removed outlier: 4.813A pdb=" N VAL I 122 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU I 118 " --> pdb=" O VAL I 122 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY I 124 " --> pdb=" O ILE I 116 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 128 through 129 removed outlier: 3.906A pdb=" N VAL I 129 " --> pdb=" O ARG I 132 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 186 through 188 Processing sheet with id=AH6, first strand: chain 'I' and resid 215 through 217 removed outlier: 9.617A pdb=" N VAL I 224 " --> pdb=" O TRP I 244 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N TRP I 244 " --> pdb=" O VAL I 224 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE I 226 " --> pdb=" O VAL I 242 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 2 through 8 Processing sheet with id=AH8, first strand: chain 'J' and resid 15 through 19 removed outlier: 3.551A pdb=" N VAL J 27 " --> pdb=" O VAL J 19 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET J 132 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR J 36 " --> pdb=" O GLN J 130 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLN J 130 " --> pdb=" O THR J 36 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL J 133 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA J 145 " --> pdb=" O VAL J 133 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TYR J 137 " --> pdb=" O SER J 141 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N SER J 141 " --> pdb=" O TYR J 137 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 41 through 48 removed outlier: 7.051A pdb=" N ALA J 121 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE J 47 " --> pdb=" O ALA J 119 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA J 119 " --> pdb=" O ILE J 47 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU J 184 " --> pdb=" O TYR J 181 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 51 through 54 Processing sheet with id=AI2, first strand: chain 'J' and resid 81 through 82 Processing sheet with id=AI3, first strand: chain 'J' and resid 204 through 206 Processing sheet with id=AI4, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AI5, first strand: chain 'J' and resid 261 through 262 Processing sheet with id=AI6, first strand: chain 'J' and resid 301 through 306 removed outlier: 5.958A pdb=" N CYS J 302 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ALA J 320 " --> pdb=" O CYS J 302 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ILE J 304 " --> pdb=" O THR J 318 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR J 318 " --> pdb=" O ILE J 304 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'J' and resid 344 through 347 removed outlier: 3.749A pdb=" N GLY J 327 " --> pdb=" O LEU J 347 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 388 through 389 Processing sheet with id=AI9, first strand: chain 'K' and resid 17 through 18 removed outlier: 3.655A pdb=" N ALA K 17 " --> pdb=" O SER K 29 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 34 through 37 removed outlier: 3.736A pdb=" N GLN K 48 " --> pdb=" O GLU K 34 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL K 36 " --> pdb=" O ARG K 46 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG K 46 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N SER K 50 " --> pdb=" O MET K 68 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N MET K 68 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR K 72 " --> pdb=" O ASN K 69 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 34 through 37 removed outlier: 3.736A pdb=" N GLN K 48 " --> pdb=" O GLU K 34 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL K 36 " --> pdb=" O ARG K 46 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG K 46 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR K 97 " --> pdb=" O THR K 49 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N ALA K 51 " --> pdb=" O HIS K 95 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N HIS K 95 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N PHE K 53 " --> pdb=" O SER K 93 " (cutoff:3.500A) removed outlier: 10.696A pdb=" N SER K 93 " --> pdb=" O PHE K 53 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'K' and resid 81 through 84 Processing sheet with id=AJ4, first strand: chain 'K' and resid 146 through 153 Processing sheet with id=AJ5, first strand: chain 'K' and resid 163 through 164 Processing sheet with id=AJ6, first strand: chain 'K' and resid 166 through 167 Processing sheet with id=AJ7, first strand: chain 'K' and resid 178 through 180 Processing sheet with id=AJ8, first strand: chain 'K' and resid 207 through 208 removed outlier: 3.645A pdb=" N GLY K 207 " --> pdb=" O TYR K 197 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'K' and resid 272 through 276 removed outlier: 3.519A pdb=" N THR K 279 " --> pdb=" O LYS K 276 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'L' and resid 133 through 134 removed outlier: 5.249A pdb=" N VAL L 122 " --> pdb=" O LEU L 118 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU L 118 " --> pdb=" O VAL L 122 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY L 124 " --> pdb=" O ILE L 116 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'L' and resid 186 through 188 Processing sheet with id=AK3, first strand: chain 'L' and resid 215 through 217 removed outlier: 6.613A pdb=" N ILE L 216 " --> pdb=" O VAL L 224 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N VAL L 224 " --> pdb=" O TRP L 244 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TRP L 244 " --> pdb=" O VAL L 224 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE L 226 " --> pdb=" O VAL L 242 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER L 240 " --> pdb=" O LEU L 228 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'M' and resid 197 through 199 Processing sheet with id=AK5, first strand: chain 'N' and resid 197 through 199 Processing sheet with id=AK6, first strand: chain 'O' and resid 197 through 201 removed outlier: 7.009A pdb=" N SER O 204 " --> pdb=" O CYS O 200 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'P' and resid 197 through 201 removed outlier: 3.532A pdb=" N CYS P 200 " --> pdb=" O SER P 204 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N SER P 204 " --> pdb=" O CYS P 200 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'Q' and resid 117 through 120 removed outlier: 3.724A pdb=" N GLN Q 126 " --> pdb=" O CYS Q 120 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'R' and resid 117 through 120 removed outlier: 3.781A pdb=" N GLN R 126 " --> pdb=" O CYS R 120 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'S' and resid 117 through 120 removed outlier: 4.569A pdb=" N GLN S 126 " --> pdb=" O CYS S 120 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'T' and resid 117 through 120 removed outlier: 4.169A pdb=" N GLN T 126 " --> pdb=" O CYS T 120 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2280 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.27 Time building geometry restraints manager: 3.53 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: 11064 1.34 - 1.46: 8044 1.46 - 1.59: 15319 1.59 - 1.71: 1 1.71 - 1.83: 284 Bond restraints: 34712 Sorted by residual: bond pdb=" CA ASP J 312 " pdb=" C ASP J 312 " ideal model delta sigma weight residual 1.522 1.566 -0.044 1.23e-02 6.61e+03 1.27e+01 bond pdb=" C PRO K 169 " pdb=" N GLY K 170 " ideal model delta sigma weight residual 1.330 1.290 0.039 1.31e-02 5.83e+03 9.02e+00 bond pdb=" CA PRO B 169 " pdb=" C PRO B 169 " ideal model delta sigma weight residual 1.520 1.553 -0.034 1.31e-02 5.83e+03 6.68e+00 bond pdb=" CA PRO I 115 " pdb=" C PRO I 115 " ideal model delta sigma weight residual 1.524 1.550 -0.026 1.11e-02 8.12e+03 5.69e+00 bond pdb=" CB ASN L 187 " pdb=" CG ASN L 187 " ideal model delta sigma weight residual 1.516 1.572 -0.056 2.50e-02 1.60e+03 5.03e+00 ... (remaining 34707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 46803 3.16 - 6.33: 418 6.33 - 9.49: 58 9.49 - 12.65: 11 12.65 - 15.82: 2 Bond angle restraints: 47292 Sorted by residual: angle pdb=" N LYS J 61 " pdb=" CA LYS J 61 " pdb=" C LYS J 61 " ideal model delta sigma weight residual 108.20 92.38 15.82 1.71e+00 3.42e-01 8.56e+01 angle pdb=" N THR A 153 " pdb=" CA THR A 153 " pdb=" C THR A 153 " ideal model delta sigma weight residual 109.72 118.99 -9.27 1.25e+00 6.40e-01 5.50e+01 angle pdb=" N LYS H 156 " pdb=" CA LYS H 156 " pdb=" C LYS H 156 " ideal model delta sigma weight residual 109.46 121.40 -11.94 1.66e+00 3.63e-01 5.17e+01 angle pdb=" N GLU A 152 " pdb=" CA GLU A 152 " pdb=" C GLU A 152 " ideal model delta sigma weight residual 111.28 118.96 -7.68 1.09e+00 8.42e-01 4.97e+01 angle pdb=" O ASP K 229 " pdb=" C ASP K 229 " pdb=" N ASN K 230 " ideal model delta sigma weight residual 123.05 115.89 7.16 1.19e+00 7.06e-01 3.62e+01 ... (remaining 47287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 17706 18.01 - 36.03: 2377 36.03 - 54.04: 630 54.04 - 72.06: 130 72.06 - 90.07: 37 Dihedral angle restraints: 20880 sinusoidal: 8260 harmonic: 12620 Sorted by residual: dihedral pdb=" CB CYS A 68 " pdb=" SG CYS A 68 " pdb=" SG CYS A 78 " pdb=" CB CYS A 78 " ideal model delta sinusoidal sigma weight residual -86.00 -176.07 90.07 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS R 134 " pdb=" SG CYS R 134 " pdb=" SG CYS R 149 " pdb=" CB CYS R 149 " ideal model delta sinusoidal sigma weight residual 93.00 4.17 88.83 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual -86.00 -9.76 -76.24 1 1.00e+01 1.00e-02 7.32e+01 ... (remaining 20877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4461 0.073 - 0.146: 707 0.146 - 0.219: 55 0.219 - 0.292: 12 0.292 - 0.365: 5 Chirality restraints: 5240 Sorted by residual: chirality pdb=" CA LYS J 61 " pdb=" N LYS J 61 " pdb=" C LYS J 61 " pdb=" CB LYS J 61 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA LYS H 156 " pdb=" N LYS H 156 " pdb=" C LYS H 156 " pdb=" CB LYS H 156 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA TYR H 64 " pdb=" N TYR H 64 " pdb=" C TYR H 64 " pdb=" CB TYR H 64 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 5237 not shown) Planarity restraints: 6128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 182 " -0.094 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO C 183 " 0.243 5.00e-02 4.00e+02 pdb=" CA PRO C 183 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO C 183 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 311 " 0.025 2.00e-02 2.50e+03 5.23e-02 2.74e+01 pdb=" C PHE J 311 " -0.090 2.00e-02 2.50e+03 pdb=" O PHE J 311 " 0.036 2.00e-02 2.50e+03 pdb=" N ASP J 312 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP K 229 " 0.020 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ASP K 229 " -0.066 2.00e-02 2.50e+03 pdb=" O ASP K 229 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN K 230 " 0.022 2.00e-02 2.50e+03 ... (remaining 6125 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 325 2.59 - 3.16: 24674 3.16 - 3.74: 49332 3.74 - 4.32: 65336 4.32 - 4.90: 113724 Nonbonded interactions: 253391 Sorted by model distance: nonbonded pdb=" OD1 ASP E 1 " pdb=" N LEU E 2 " model vdw 2.007 3.120 nonbonded pdb=" N GLU J 184 " pdb=" OE1 GLU J 184 " model vdw 2.078 3.120 nonbonded pdb=" NZ LYS K 156 " pdb=" OD2 ASP P 213 " model vdw 2.106 3.120 nonbonded pdb=" NZ LYS H 206 " pdb=" OD2 ASP S 135 " model vdw 2.116 3.120 nonbonded pdb=" OD1 ASP B 1 " pdb=" N LEU B 2 " model vdw 2.132 3.120 ... (remaining 253386 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' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 32.260 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 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 : 0.005 0.406 34796 Z= 0.235 Angle : 0.846 32.873 47460 Z= 0.464 Chirality : 0.054 0.365 5240 Planarity : 0.008 0.140 6128 Dihedral : 17.344 89.752 12540 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.24 % Allowed : 32.45 % Favored : 67.31 % 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 aren not related in a simple way. whole: -2.77 (0.12), residues: 4336 helix: -3.85 (0.13), residues: 396 sheet: -0.70 (0.16), residues: 1188 loop : -2.15 (0.10), residues: 2752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG K 390 TYR 0.034 0.002 TYR A 309 PHE 0.047 0.002 PHE G 421 TRP 0.021 0.001 TRP D 410 HIS 0.027 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00453 (34712) covalent geometry : angle 0.81801 (47292) SS BOND : bond 0.04777 ( 84) SS BOND : angle 3.71304 ( 168) hydrogen bonds : bond 0.28045 ( 862) hydrogen bonds : angle 9.60960 ( 2280) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 353 time to evaluate : 1.325 Fit side-chains REVERT: A 383 PRO cc_start: 0.8760 (Cg_exo) cc_final: 0.8539 (Cg_endo) REVERT: H 8 GLN cc_start: 0.8407 (mp10) cc_final: 0.8080 (mp10) REVERT: H 205 ARG cc_start: 0.6505 (tpp80) cc_final: 0.6083 (mmm160) REVERT: L 195 TYR cc_start: 0.5458 (t80) cc_final: 0.5040 (t80) outliers start: 9 outliers final: 2 residues processed: 361 average time/residue: 0.2164 time to fit residues: 128.3881 Evaluate side-chains 316 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain H residue 346 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 40.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 236 GLN B 8 GLN B 95 HIS B 168 GLN B 253 HIS D 223 GLN D 363 HIS D 369 GLN E 144 HIS E 155 HIS E 168 GLN E 230 ASN E 253 HIS E 338 GLN ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 176 GLN F 189 HIS F 246 GLN G 30 GLN G 130 GLN G 328 ASN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS H 404 GLN I 119 ASN J 35 ASN ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 223 GLN J 439 HIS K 94 HIS K 194 GLN L 119 ASN R 151 ASN S 116 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.158738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.119093 restraints weight = 47774.584| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.32 r_work: 0.2956 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 34796 Z= 0.231 Angle : 0.672 12.745 47460 Z= 0.355 Chirality : 0.048 0.254 5240 Planarity : 0.006 0.084 6128 Dihedral : 5.923 75.885 4724 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 5.15 % Allowed : 28.74 % Favored : 66.11 % 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 aren not related in a simple way. whole: -2.29 (0.12), residues: 4336 helix: -1.55 (0.23), residues: 396 sheet: -0.63 (0.16), residues: 1136 loop : -2.01 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 119 TYR 0.027 0.002 TYR A 309 PHE 0.040 0.002 PHE J 311 TRP 0.019 0.002 TRP L 188 HIS 0.013 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00558 (34712) covalent geometry : angle 0.66929 (47292) SS BOND : bond 0.00434 ( 84) SS BOND : angle 1.18942 ( 168) hydrogen bonds : bond 0.05552 ( 862) hydrogen bonds : angle 6.20295 ( 2280) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 329 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.9295 (ptm) cc_final: 0.8928 (ptm) REVERT: B 168 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8490 (tt0) REVERT: B 357 TYR cc_start: 0.8900 (t80) cc_final: 0.8677 (t80) REVERT: B 384 TRP cc_start: 0.7020 (t60) cc_final: 0.6813 (t-100) REVERT: B 398 LYS cc_start: 0.8191 (tttm) cc_final: 0.7957 (tttm) REVERT: C 117 MET cc_start: 0.7995 (mmp) cc_final: 0.7787 (mmp) REVERT: C 121 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.7075 (pm20) REVERT: C 217 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7917 (mm) REVERT: D 434 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6602 (mp) REVERT: E 41 HIS cc_start: 0.9128 (OUTLIER) cc_final: 0.7190 (t70) REVERT: E 199 CYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8334 (m) REVERT: E 362 LEU cc_start: 0.8553 (mm) cc_final: 0.8224 (tp) REVERT: F 170 MET cc_start: 0.4136 (pmm) cc_final: 0.3884 (pmm) REVERT: G 368 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8563 (pt) REVERT: H 68 MET cc_start: 0.8466 (ptm) cc_final: 0.8233 (ptp) REVERT: J 45 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8132 (mt-10) REVERT: J 125 HIS cc_start: 0.6755 (OUTLIER) cc_final: 0.5189 (t-90) REVERT: J 192 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7956 (tp30) REVERT: J 328 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8176 (t0) REVERT: J 370 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.9027 (p) REVERT: J 438 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8603 (m-80) REVERT: L 186 TYR cc_start: 0.7461 (m-80) cc_final: 0.7108 (m-80) REVERT: L 195 TYR cc_start: 0.4946 (t80) cc_final: 0.4562 (t80) REVERT: S 111 ARG cc_start: 0.4007 (OUTLIER) cc_final: 0.3061 (tpt170) outliers start: 193 outliers final: 129 residues processed: 493 average time/residue: 0.2113 time to fit residues: 174.6997 Evaluate side-chains 457 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 316 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS 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 184 GLU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL 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 371 CYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 434 LEU 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 129 GLU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 411 ILE Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 299 SER 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 346 HIS Chi-restraints excluded: chain H residue 371 CYS Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 393 CYS Chi-restraints excluded: chain H residue 412 LEU Chi-restraints excluded: chain I residue 138 HIS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 282 ASP Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain J residue 328 ASN Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain J residue 438 PHE Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 346 HIS Chi-restraints excluded: chain K residue 382 SER Chi-restraints excluded: chain K residue 413 CYS Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 237 THR Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 111 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 69 optimal weight: 0.0570 chunk 56 optimal weight: 5.9990 chunk 361 optimal weight: 2.9990 chunk 185 optimal weight: 0.0870 chunk 269 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 314 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 326 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 361 ASN D 369 GLN E 155 HIS E 168 GLN ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 GLN G 332 HIS ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 GLN J 100 ASN K 175 HIS K 253 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.163491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124443 restraints weight = 47458.235| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.22 r_work: 0.3108 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 34796 Z= 0.102 Angle : 0.556 11.656 47460 Z= 0.291 Chirality : 0.043 0.201 5240 Planarity : 0.004 0.062 6128 Dihedral : 5.422 73.789 4724 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.17 % Allowed : 29.70 % Favored : 66.13 % 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 aren not related in a simple way. whole: -1.90 (0.12), residues: 4336 helix: 0.06 (0.27), residues: 372 sheet: -0.59 (0.16), residues: 1160 loop : -1.83 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 205 TYR 0.016 0.001 TYR A 309 PHE 0.016 0.001 PHE G 311 TRP 0.017 0.001 TRP L 188 HIS 0.004 0.001 HIS G 125 Details of bonding type rmsd covalent geometry : bond 0.00232 (34712) covalent geometry : angle 0.55436 (47292) SS BOND : bond 0.00243 ( 84) SS BOND : angle 0.94136 ( 168) hydrogen bonds : bond 0.04110 ( 862) hydrogen bonds : angle 5.45914 ( 2280) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 339 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 ILE cc_start: 0.8825 (mt) cc_final: 0.8594 (tp) REVERT: B 221 LYS cc_start: 0.8984 (mtmm) cc_final: 0.8652 (mtmm) REVERT: B 398 LYS cc_start: 0.8012 (tttm) cc_final: 0.7797 (tttm) REVERT: C 121 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.7008 (pm20) REVERT: D 99 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7322 (tm-30) REVERT: D 282 ASP cc_start: 0.8896 (t70) cc_final: 0.8633 (t0) REVERT: D 316 ILE cc_start: 0.8471 (mt) cc_final: 0.8255 (tp) REVERT: D 410 TRP cc_start: 0.8402 (m100) cc_final: 0.7974 (m100) REVERT: E 41 HIS cc_start: 0.8920 (OUTLIER) cc_final: 0.8382 (t70) REVERT: E 199 CYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8278 (m) REVERT: G 368 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8675 (pt) REVERT: H 284 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8910 (mt) REVERT: H 310 ARG cc_start: 0.8349 (mtm110) cc_final: 0.7920 (mtm-85) REVERT: J 299 ASP cc_start: 0.8512 (t70) cc_final: 0.8302 (t70) REVERT: J 370 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8891 (p) REVERT: J 438 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8547 (m-80) REVERT: K 168 GLN cc_start: 0.8908 (tt0) cc_final: 0.8615 (tt0) REVERT: K 222 GLN cc_start: 0.8487 (pt0) cc_final: 0.7769 (pm20) REVERT: L 195 TYR cc_start: 0.4981 (t80) cc_final: 0.4572 (t80) REVERT: L 209 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7099 (tmtt) REVERT: L 214 ARG cc_start: 0.8696 (mmt90) cc_final: 0.8437 (mmt90) REVERT: S 111 ARG cc_start: 0.4071 (OUTLIER) cc_final: 0.3137 (tpt170) REVERT: S 137 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.5806 (pm20) outliers start: 156 outliers final: 96 residues processed: 475 average time/residue: 0.2110 time to fit residues: 167.2920 Evaluate side-chains 424 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 318 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 GLN 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 208 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 411 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 24 HIS Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 346 HIS Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 393 CYS Chi-restraints excluded: chain H residue 412 LEU Chi-restraints excluded: chain I residue 138 HIS Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 253 ASN Chi-restraints excluded: chain J residue 282 ASP Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain J residue 438 PHE Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 209 LYS Chi-restraints excluded: chain L residue 237 THR Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain P residue 198 PHE Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 111 ARG Chi-restraints excluded: chain S residue 137 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 145 optimal weight: 20.0000 chunk 386 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 274 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 345 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 380 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 168 GLN D 369 GLN E 222 GLN ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS J 439 HIS K 41 HIS K 155 HIS K 194 GLN N 199 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.154468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.114738 restraints weight = 47373.318| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.31 r_work: 0.2959 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 34796 Z= 0.278 Angle : 0.696 10.516 47460 Z= 0.365 Chirality : 0.049 0.205 5240 Planarity : 0.005 0.069 6128 Dihedral : 5.883 73.685 4722 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 7.51 % Allowed : 26.95 % Favored : 65.54 % 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 aren not related in a simple way. whole: -1.94 (0.12), residues: 4336 helix: 0.40 (0.27), residues: 372 sheet: -0.73 (0.15), residues: 1216 loop : -1.89 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 205 TYR 0.029 0.002 TYR A 309 PHE 0.053 0.002 PHE J 311 TRP 0.019 0.002 TRP L 188 HIS 0.009 0.001 HIS G 125 Details of bonding type rmsd covalent geometry : bond 0.00681 (34712) covalent geometry : angle 0.69331 (47292) SS BOND : bond 0.00460 ( 84) SS BOND : angle 1.31415 ( 168) hydrogen bonds : bond 0.04709 ( 862) hydrogen bonds : angle 5.59099 ( 2280) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 281 poor density : 317 time to evaluate : 1.289 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 103 MET cc_start: 0.8869 (tpt) cc_final: 0.8645 (tpt) REVERT: B 168 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: B 200 LYS cc_start: 0.8153 (tppp) cc_final: 0.7806 (ttmt) REVERT: B 280 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8876 (tt) REVERT: B 384 TRP cc_start: 0.7146 (t60) cc_final: 0.6789 (t-100) REVERT: C 217 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7874 (mm) REVERT: D 99 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7295 (tm-30) REVERT: D 282 ASP cc_start: 0.8804 (t70) cc_final: 0.8494 (t0) REVERT: D 316 ILE cc_start: 0.8366 (mt) cc_final: 0.8056 (tp) REVERT: D 436 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7467 (mp) REVERT: E 19 CYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8697 (t) REVERT: E 41 HIS cc_start: 0.9160 (OUTLIER) cc_final: 0.7322 (t70) REVERT: E 199 CYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8094 (m) REVERT: E 308 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.9024 (mm) REVERT: F 188 TRP cc_start: 0.6911 (t-100) cc_final: 0.6624 (t-100) REVERT: F 200 PHE cc_start: 0.5644 (t80) cc_final: 0.5431 (t80) REVERT: G 107 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6897 (t80) REVERT: G 368 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8573 (pt) REVERT: H 284 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8837 (mt) REVERT: H 300 ASP cc_start: 0.8145 (t0) cc_final: 0.7322 (p0) REVERT: I 169 CYS cc_start: 0.2281 (OUTLIER) cc_final: 0.2070 (t) REVERT: I 185 PHE cc_start: 0.4189 (OUTLIER) cc_final: 0.3347 (t80) REVERT: J 29 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9048 (tp) REVERT: J 45 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8421 (mm-30) REVERT: J 125 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.5335 (t-90) REVERT: J 159 ASP cc_start: 0.8646 (t0) cc_final: 0.8318 (t0) REVERT: J 370 VAL cc_start: 0.9249 (OUTLIER) cc_final: 0.9023 (p) REVERT: K 222 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: L 195 TYR cc_start: 0.5300 (t80) cc_final: 0.4720 (t80) REVERT: L 209 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7717 (tmtt) REVERT: L 245 ASN cc_start: 0.8589 (p0) cc_final: 0.8144 (p0) REVERT: N 199 GLN cc_start: 0.6558 (OUTLIER) cc_final: 0.6344 (tm-30) outliers start: 281 outliers final: 201 residues processed: 556 average time/residue: 0.1967 time to fit residues: 182.9680 Evaluate side-chains 525 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 305 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 156 LYS 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 208 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 409 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 240 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain E residue 19 CYS 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 133 VAL Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 223 CYS Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 107 TYR Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 411 ILE Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain G residue 438 PHE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 346 HIS Chi-restraints excluded: chain H residue 365 ILE Chi-restraints excluded: chain H residue 371 CYS Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 393 CYS Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain I residue 138 HIS Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 211 SER 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 282 ASP Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 222 GLN Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 346 HIS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 389 THR Chi-restraints excluded: chain K residue 413 CYS Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 209 LYS Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 237 THR Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain N residue 199 GLN Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain P residue 198 PHE Chi-restraints excluded: chain P residue 209 SER Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 134 CYS Chi-restraints excluded: chain S residue 111 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 260 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 245 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 265 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 391 optimal weight: 5.9990 chunk 238 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 369 GLN D 226 GLN D 369 GLN E 114 HIS E 222 GLN E 358 ASN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 439 HIS K 41 HIS K 155 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.158089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.117902 restraints weight = 47583.942| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.19 r_work: 0.2949 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34796 Z= 0.152 Angle : 0.601 10.609 47460 Z= 0.314 Chirality : 0.045 0.191 5240 Planarity : 0.005 0.070 6128 Dihedral : 5.616 73.024 4722 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 5.96 % Allowed : 28.37 % Favored : 65.68 % 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 aren not related in a simple way. whole: -1.81 (0.12), residues: 4336 helix: 0.87 (0.28), residues: 372 sheet: -0.64 (0.15), residues: 1160 loop : -1.83 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 205 TYR 0.022 0.001 TYR A 309 PHE 0.029 0.001 PHE J 311 TRP 0.021 0.001 TRP L 188 HIS 0.019 0.001 HIS K 41 Details of bonding type rmsd covalent geometry : bond 0.00367 (34712) covalent geometry : angle 0.59703 (47292) SS BOND : bond 0.00296 ( 84) SS BOND : angle 1.24434 ( 168) hydrogen bonds : bond 0.03948 ( 862) hydrogen bonds : angle 5.30473 ( 2280) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 318 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8863 (tpt) cc_final: 0.8655 (tpt) REVERT: A 107 TYR cc_start: 0.6485 (OUTLIER) cc_final: 0.5609 (t80) REVERT: B 31 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.7999 (tp) REVERT: B 398 LYS cc_start: 0.8025 (tttm) cc_final: 0.7804 (tttm) REVERT: C 217 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7888 (mm) REVERT: D 99 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7223 (tm-30) REVERT: D 282 ASP cc_start: 0.8769 (t70) cc_final: 0.8472 (t0) REVERT: D 316 ILE cc_start: 0.8328 (mt) cc_final: 0.8052 (tp) REVERT: E 19 CYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8695 (t) REVERT: E 41 HIS cc_start: 0.9074 (OUTLIER) cc_final: 0.7020 (t70) REVERT: E 199 CYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8121 (m) REVERT: E 213 HIS cc_start: 0.8000 (t-90) cc_final: 0.7780 (t-90) REVERT: G 368 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8421 (pt) REVERT: H 27 CYS cc_start: 0.7897 (m) cc_final: 0.7390 (p) REVERT: H 50 SER cc_start: 0.9162 (OUTLIER) cc_final: 0.8916 (p) REVERT: H 284 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8853 (mt) REVERT: H 300 ASP cc_start: 0.8097 (t0) cc_final: 0.7265 (p0) REVERT: I 185 PHE cc_start: 0.3697 (OUTLIER) cc_final: 0.2534 (t80) REVERT: J 125 HIS cc_start: 0.6712 (OUTLIER) cc_final: 0.5062 (t-90) REVERT: J 159 ASP cc_start: 0.8703 (t0) cc_final: 0.8424 (t0) REVERT: J 370 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8928 (p) REVERT: J 421 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7347 (t80) REVERT: K 168 GLN cc_start: 0.8941 (tt0) cc_final: 0.8610 (tt0) REVERT: K 222 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: L 195 TYR cc_start: 0.5492 (t80) cc_final: 0.4836 (t80) REVERT: L 209 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7560 (tmtt) REVERT: L 245 ASN cc_start: 0.8513 (p0) cc_final: 0.8227 (p0) REVERT: S 111 ARG cc_start: 0.4365 (OUTLIER) cc_final: 0.3182 (tpt170) outliers start: 223 outliers final: 171 residues processed: 505 average time/residue: 0.1992 time to fit residues: 168.9172 Evaluate side-chains 496 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 309 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 175 ASP 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 208 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 223 CYS Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 411 ILE Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain G residue 438 PHE Chi-restraints excluded: chain H residue 24 HIS Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 346 HIS Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 393 CYS Chi-restraints excluded: chain H residue 412 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 138 HIS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 211 SER 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 282 ASP Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain J residue 439 HIS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 222 GLN Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 346 HIS Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 209 LYS Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 237 THR Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain P residue 206 ILE Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 134 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 111 ARG Chi-restraints excluded: chain T residue 130 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 128 optimal weight: 7.9990 chunk 347 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 chunk 378 optimal weight: 8.9990 chunk 360 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 195 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 GLN D 369 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 439 HIS K 155 HIS K 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.155230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.115421 restraints weight = 47229.150| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.22 r_work: 0.2975 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 34796 Z= 0.214 Angle : 0.639 9.860 47460 Z= 0.334 Chirality : 0.047 0.193 5240 Planarity : 0.005 0.074 6128 Dihedral : 5.710 72.871 4722 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 7.29 % Allowed : 27.19 % Favored : 65.52 % 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 aren not related in a simple way. whole: -1.83 (0.12), residues: 4336 helix: 0.95 (0.28), residues: 372 sheet: -0.66 (0.15), residues: 1152 loop : -1.86 (0.11), residues: 2812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 205 TYR 0.027 0.002 TYR A 309 PHE 0.041 0.002 PHE J 311 TRP 0.021 0.001 TRP L 188 HIS 0.017 0.001 HIS J 439 Details of bonding type rmsd covalent geometry : bond 0.00526 (34712) covalent geometry : angle 0.63469 (47292) SS BOND : bond 0.00345 ( 84) SS BOND : angle 1.35523 ( 168) hydrogen bonds : bond 0.04122 ( 862) hydrogen bonds : angle 5.31210 ( 2280) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 273 poor density : 313 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.6684 (OUTLIER) cc_final: 0.5752 (t80) REVERT: B 31 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8082 (tp) REVERT: B 398 LYS cc_start: 0.8109 (tttm) cc_final: 0.7898 (tttm) REVERT: C 217 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7961 (mm) REVERT: D 99 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7277 (tm-30) REVERT: D 282 ASP cc_start: 0.8772 (t70) cc_final: 0.8474 (t0) REVERT: D 316 ILE cc_start: 0.8330 (mt) cc_final: 0.8043 (tp) REVERT: D 436 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7602 (mp) REVERT: E 19 CYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8789 (t) REVERT: E 41 HIS cc_start: 0.9107 (OUTLIER) cc_final: 0.7090 (t70) REVERT: E 199 CYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8159 (m) REVERT: E 213 HIS cc_start: 0.8033 (t-90) cc_final: 0.7803 (t-90) REVERT: E 308 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8992 (mm) REVERT: E 388 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6399 (mtp180) REVERT: F 188 TRP cc_start: 0.6797 (t-100) cc_final: 0.6482 (t-100) REVERT: G 368 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8499 (pt) REVERT: H 27 CYS cc_start: 0.8190 (m) cc_final: 0.7654 (p) REVERT: H 50 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8922 (p) REVERT: H 284 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8857 (mt) REVERT: H 300 ASP cc_start: 0.8139 (t0) cc_final: 0.7346 (p0) REVERT: I 185 PHE cc_start: 0.3841 (OUTLIER) cc_final: 0.2510 (t80) REVERT: J 29 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9024 (tp) REVERT: J 125 HIS cc_start: 0.6812 (OUTLIER) cc_final: 0.5116 (t-90) REVERT: J 159 ASP cc_start: 0.8781 (t0) cc_final: 0.8524 (t0) REVERT: J 421 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7421 (t80) REVERT: K 168 GLN cc_start: 0.8940 (tt0) cc_final: 0.8607 (tt0) REVERT: K 222 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: L 188 TRP cc_start: 0.7364 (OUTLIER) cc_final: 0.5003 (t-100) REVERT: L 195 TYR cc_start: 0.5657 (t80) cc_final: 0.4990 (t80) REVERT: L 209 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7675 (tmtt) REVERT: L 245 ASN cc_start: 0.8510 (p0) cc_final: 0.8248 (p0) REVERT: P 220 ASP cc_start: 0.6407 (OUTLIER) cc_final: 0.6039 (p0) outliers start: 273 outliers final: 219 residues processed: 547 average time/residue: 0.1965 time to fit residues: 181.3445 Evaluate side-chains 549 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 310 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 156 LYS 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 208 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 409 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 240 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 223 CYS Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 388 ARG Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain G residue 359 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 408 TRP Chi-restraints excluded: chain G residue 411 ILE Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain G residue 438 PHE Chi-restraints excluded: chain H residue 24 HIS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 346 HIS Chi-restraints excluded: chain H residue 371 CYS Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 393 CYS Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 138 HIS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 211 SER 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 282 ASP Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain J residue 439 HIS Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 222 GLN Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 346 HIS Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 389 THR Chi-restraints excluded: chain K residue 413 CYS Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 209 LYS Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 237 THR Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain P residue 206 ILE Chi-restraints excluded: chain P residue 220 ASP Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 111 ARG Chi-restraints excluded: chain T residue 130 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 62 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 chunk 417 optimal weight: 0.0570 chunk 288 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 427 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 130 GLN B 168 GLN D 369 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 439 HIS K 155 HIS N 199 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.157102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.117231 restraints weight = 47390.181| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.16 r_work: 0.3008 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34796 Z= 0.171 Angle : 0.610 9.652 47460 Z= 0.318 Chirality : 0.046 0.194 5240 Planarity : 0.005 0.073 6128 Dihedral : 5.617 72.662 4722 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 7.18 % Allowed : 27.62 % Favored : 65.20 % 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 aren not related in a simple way. whole: -1.77 (0.12), residues: 4336 helix: 1.08 (0.29), residues: 372 sheet: -0.69 (0.15), residues: 1238 loop : -1.83 (0.11), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 205 TYR 0.024 0.001 TYR A 309 PHE 0.032 0.001 PHE J 311 TRP 0.020 0.001 TRP L 188 HIS 0.014 0.001 HIS J 439 Details of bonding type rmsd covalent geometry : bond 0.00415 (34712) covalent geometry : angle 0.60711 (47292) SS BOND : bond 0.00291 ( 84) SS BOND : angle 1.23863 ( 168) hydrogen bonds : bond 0.03885 ( 862) hydrogen bonds : angle 5.20525 ( 2280) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 317 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.6648 (OUTLIER) cc_final: 0.5776 (t80) REVERT: A 190 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7913 (m-10) REVERT: B 31 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8104 (tp) REVERT: C 217 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7966 (mm) REVERT: D 99 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7327 (tm-30) REVERT: D 282 ASP cc_start: 0.8737 (t70) cc_final: 0.8470 (t0) REVERT: D 316 ILE cc_start: 0.8385 (mt) cc_final: 0.8142 (tp) REVERT: D 436 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7650 (mp) REVERT: E 19 CYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8740 (t) REVERT: E 41 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.7018 (t70) REVERT: E 199 CYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8096 (m) REVERT: E 308 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8973 (mm) REVERT: E 388 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6319 (mtp180) REVERT: F 188 TRP cc_start: 0.6793 (t-100) cc_final: 0.6490 (t-100) REVERT: G 368 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8570 (pt) REVERT: G 437 PHE cc_start: 0.8067 (t80) cc_final: 0.7788 (t80) REVERT: H 50 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8919 (p) REVERT: H 284 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8881 (mt) REVERT: H 300 ASP cc_start: 0.8148 (t0) cc_final: 0.7397 (p0) REVERT: I 185 PHE cc_start: 0.3922 (OUTLIER) cc_final: 0.2448 (t80) REVERT: J 29 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8996 (tp) REVERT: J 125 HIS cc_start: 0.6788 (OUTLIER) cc_final: 0.5137 (t-90) REVERT: J 159 ASP cc_start: 0.8585 (t0) cc_final: 0.8355 (t0) REVERT: J 421 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7380 (t80) REVERT: K 168 GLN cc_start: 0.8919 (tt0) cc_final: 0.8626 (tt0) REVERT: K 222 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7665 (pm20) REVERT: L 188 TRP cc_start: 0.7378 (OUTLIER) cc_final: 0.5082 (t-100) REVERT: L 209 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7654 (tmtt) REVERT: L 245 ASN cc_start: 0.8491 (p0) cc_final: 0.8208 (p0) REVERT: P 220 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6236 (p0) REVERT: S 111 ARG cc_start: 0.4474 (OUTLIER) cc_final: 0.3393 (tpt170) outliers start: 269 outliers final: 220 residues processed: 547 average time/residue: 0.1948 time to fit residues: 180.1559 Evaluate side-chains 549 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 307 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 156 LYS 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 190 PHE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 412 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 240 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 LEU 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 107 TYR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 223 CYS Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 388 ARG Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain G residue 359 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 408 TRP Chi-restraints excluded: chain G residue 411 ILE Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain G residue 438 PHE Chi-restraints excluded: chain H residue 24 HIS Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 305 ARG Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 346 HIS Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 393 CYS Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 138 HIS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 211 ASP Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 211 SER 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 282 ASP Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain J residue 439 HIS Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 222 GLN Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 346 HIS Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 389 THR Chi-restraints excluded: chain K residue 413 CYS Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 209 LYS Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 237 THR Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain P residue 206 ILE Chi-restraints excluded: chain P residue 209 SER Chi-restraints excluded: chain P residue 220 ASP Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 134 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 111 ARG Chi-restraints excluded: chain T residue 130 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 354 optimal weight: 9.9990 chunk 182 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 18 optimal weight: 0.0570 chunk 262 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 229 optimal weight: 5.9990 chunk 385 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 overall best weight: 3.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN D 226 GLN D 369 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.155993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116003 restraints weight = 47135.707| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.24 r_work: 0.2982 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34796 Z= 0.177 Angle : 0.619 9.444 47460 Z= 0.322 Chirality : 0.046 0.213 5240 Planarity : 0.005 0.076 6128 Dihedral : 5.600 72.699 4722 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 7.35 % Allowed : 27.43 % Favored : 65.22 % 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 aren not related in a simple way. whole: -1.75 (0.12), residues: 4336 helix: 1.15 (0.28), residues: 372 sheet: -0.62 (0.15), residues: 1164 loop : -1.83 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 205 TYR 0.024 0.002 TYR A 309 PHE 0.033 0.002 PHE J 311 TRP 0.020 0.001 TRP L 188 HIS 0.007 0.001 HIS G 125 Details of bonding type rmsd covalent geometry : bond 0.00432 (34712) covalent geometry : angle 0.61493 (47292) SS BOND : bond 0.00304 ( 84) SS BOND : angle 1.29881 ( 168) hydrogen bonds : bond 0.03923 ( 862) hydrogen bonds : angle 5.17017 ( 2280) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 275 poor density : 310 time to evaluate : 1.390 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 107 TYR cc_start: 0.6619 (OUTLIER) cc_final: 0.5712 (t80) REVERT: A 190 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7929 (m-10) REVERT: B 31 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8091 (tp) REVERT: B 398 LYS cc_start: 0.8018 (tttm) cc_final: 0.7792 (tttm) REVERT: C 217 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7956 (mm) REVERT: D 99 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7284 (tm-30) REVERT: D 282 ASP cc_start: 0.8709 (t70) cc_final: 0.8446 (t0) REVERT: D 316 ILE cc_start: 0.8303 (mt) cc_final: 0.8027 (tp) REVERT: D 436 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7579 (mp) REVERT: E 19 CYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8789 (t) REVERT: E 41 HIS cc_start: 0.9048 (OUTLIER) cc_final: 0.6916 (t70) REVERT: E 199 CYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8147 (m) REVERT: E 308 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8968 (mm) REVERT: E 388 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6258 (mtp180) REVERT: F 188 TRP cc_start: 0.6697 (t-100) cc_final: 0.6378 (t-100) REVERT: G 368 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8497 (pt) REVERT: G 437 PHE cc_start: 0.8026 (t80) cc_final: 0.7756 (t80) REVERT: H 50 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8903 (p) REVERT: H 284 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8873 (mt) REVERT: H 300 ASP cc_start: 0.8075 (t0) cc_final: 0.7257 (p0) REVERT: I 185 PHE cc_start: 0.4191 (OUTLIER) cc_final: 0.2754 (t80) REVERT: J 29 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.8991 (tp) REVERT: J 125 HIS cc_start: 0.6791 (OUTLIER) cc_final: 0.5087 (t-90) REVERT: J 159 ASP cc_start: 0.8734 (t0) cc_final: 0.8490 (t0) REVERT: J 190 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.6985 (m-80) REVERT: J 421 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7423 (t80) REVERT: K 168 GLN cc_start: 0.8939 (tt0) cc_final: 0.8618 (tt0) REVERT: K 222 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: L 188 TRP cc_start: 0.7226 (OUTLIER) cc_final: 0.4959 (t-100) REVERT: L 209 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7638 (tmtt) REVERT: L 245 ASN cc_start: 0.8457 (p0) cc_final: 0.8204 (p0) REVERT: P 220 ASP cc_start: 0.6527 (OUTLIER) cc_final: 0.6172 (p0) REVERT: T 144 GLU cc_start: 0.3991 (OUTLIER) cc_final: 0.3469 (pt0) outliers start: 275 outliers final: 232 residues processed: 547 average time/residue: 0.2007 time to fit residues: 184.8258 Evaluate side-chains 561 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 255 poor density : 306 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 127 CYS 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 240 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 223 CYS Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 388 ARG Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain G residue 359 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 408 TRP Chi-restraints excluded: chain G residue 411 ILE Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain G residue 438 PHE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 305 ARG Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 346 HIS Chi-restraints excluded: chain H residue 371 CYS Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 393 CYS Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 138 HIS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 211 ASP Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 190 PHE Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 211 SER 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 282 ASP Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 222 GLN Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 346 HIS Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 389 THR Chi-restraints excluded: chain K residue 413 CYS Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 209 LYS Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 237 THR Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain P residue 206 ILE Chi-restraints excluded: chain P residue 209 SER Chi-restraints excluded: chain P residue 220 ASP Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 111 ARG Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 144 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 215 optimal weight: 20.0000 chunk 329 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 293 optimal weight: 8.9990 chunk 288 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 339 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 130 GLN D 369 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 439 HIS K 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.156158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.116216 restraints weight = 47010.167| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.19 r_work: 0.2940 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34796 Z= 0.169 Angle : 0.613 10.169 47460 Z= 0.319 Chirality : 0.046 0.197 5240 Planarity : 0.005 0.077 6128 Dihedral : 5.578 72.608 4722 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 7.37 % Allowed : 27.32 % Favored : 65.30 % 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 aren not related in a simple way. whole: -1.72 (0.12), residues: 4336 helix: 1.24 (0.28), residues: 372 sheet: -0.66 (0.15), residues: 1220 loop : -1.80 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 205 TYR 0.023 0.001 TYR A 309 PHE 0.031 0.001 PHE J 311 TRP 0.020 0.001 TRP L 188 HIS 0.007 0.001 HIS G 125 Details of bonding type rmsd covalent geometry : bond 0.00412 (34712) covalent geometry : angle 0.60847 (47292) SS BOND : bond 0.00297 ( 84) SS BOND : angle 1.33041 ( 168) hydrogen bonds : bond 0.03873 ( 862) hydrogen bonds : angle 5.14457 ( 2280) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 276 poor density : 307 time to evaluate : 1.384 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 107 TYR cc_start: 0.6574 (OUTLIER) cc_final: 0.5660 (t80) REVERT: A 190 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7918 (m-10) REVERT: B 31 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8052 (tp) REVERT: B 222 GLN cc_start: 0.7823 (pm20) cc_final: 0.7506 (pm20) REVERT: C 217 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7942 (mm) REVERT: D 99 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7224 (tm-30) REVERT: D 282 ASP cc_start: 0.8693 (t70) cc_final: 0.8425 (t0) REVERT: D 316 ILE cc_start: 0.8253 (mt) cc_final: 0.7968 (tp) REVERT: D 436 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7552 (mp) REVERT: E 19 CYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8774 (t) REVERT: E 41 HIS cc_start: 0.9039 (OUTLIER) cc_final: 0.6880 (t70) REVERT: E 199 CYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8132 (m) REVERT: E 308 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8941 (mm) REVERT: E 388 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6264 (mtp180) REVERT: G 368 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8451 (pt) REVERT: G 437 PHE cc_start: 0.7999 (t80) cc_final: 0.7729 (t80) REVERT: H 21 ASN cc_start: 0.8722 (t0) cc_final: 0.8454 (t0) REVERT: H 50 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8883 (p) REVERT: H 284 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8839 (mt) REVERT: H 300 ASP cc_start: 0.7951 (t0) cc_final: 0.7156 (p0) REVERT: I 185 PHE cc_start: 0.4259 (OUTLIER) cc_final: 0.2763 (t80) REVERT: J 29 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9064 (tp) REVERT: J 125 HIS cc_start: 0.6681 (OUTLIER) cc_final: 0.5035 (t-90) REVERT: J 159 ASP cc_start: 0.8712 (t0) cc_final: 0.8450 (t0) REVERT: J 190 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.6994 (m-80) REVERT: J 421 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7428 (t80) REVERT: K 168 GLN cc_start: 0.8940 (tt0) cc_final: 0.8603 (tt0) REVERT: K 222 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: L 188 TRP cc_start: 0.7144 (OUTLIER) cc_final: 0.4952 (t-100) REVERT: L 209 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7692 (tmtt) REVERT: L 245 ASN cc_start: 0.8402 (p0) cc_final: 0.8162 (p0) REVERT: P 220 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.6216 (p0) REVERT: T 144 GLU cc_start: 0.4009 (OUTLIER) cc_final: 0.3472 (pt0) outliers start: 276 outliers final: 242 residues processed: 545 average time/residue: 0.2009 time to fit residues: 185.2071 Evaluate side-chains 568 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 265 poor density : 303 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 127 CYS 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 240 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 19 VAL 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 107 TYR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 223 CYS Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 388 ARG Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain G residue 359 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 408 TRP Chi-restraints excluded: chain G residue 411 ILE Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain G residue 438 PHE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 305 ARG Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 346 HIS Chi-restraints excluded: chain H residue 371 CYS Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 393 CYS Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 138 HIS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 211 ASP Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 190 PHE Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 211 SER 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 282 ASP Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 222 GLN Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 346 HIS Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 389 THR Chi-restraints excluded: chain K residue 413 CYS Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 209 LYS Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 237 THR Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain P residue 206 ILE Chi-restraints excluded: chain P residue 209 SER Chi-restraints excluded: chain P residue 220 ASP Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 134 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 111 ARG Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 144 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 399 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 chunk 277 optimal weight: 3.9990 chunk 197 optimal weight: 30.0000 chunk 249 optimal weight: 2.9990 chunk 347 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN D 369 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 GLN K 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.116813 restraints weight = 47311.632| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.22 r_work: 0.2951 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34796 Z= 0.158 Angle : 0.608 11.738 47460 Z= 0.316 Chirality : 0.046 0.232 5240 Planarity : 0.005 0.078 6128 Dihedral : 5.540 72.319 4722 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 6.94 % Allowed : 27.78 % Favored : 65.28 % 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 aren not related in a simple way. whole: -1.69 (0.12), residues: 4336 helix: 1.30 (0.28), residues: 372 sheet: -0.60 (0.15), residues: 1164 loop : -1.79 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 205 TYR 0.022 0.001 TYR A 309 PHE 0.029 0.001 PHE J 311 TRP 0.020 0.001 TRP L 188 HIS 0.007 0.001 HIS G 125 Details of bonding type rmsd covalent geometry : bond 0.00384 (34712) covalent geometry : angle 0.60412 (47292) SS BOND : bond 0.00278 ( 84) SS BOND : angle 1.25131 ( 168) hydrogen bonds : bond 0.03781 ( 862) hydrogen bonds : angle 5.11091 ( 2280) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8672 Ramachandran restraints generated. 4336 Oldfield, 0 Emsley, 4336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 307 time to evaluate : 1.359 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 107 TYR cc_start: 0.6527 (OUTLIER) cc_final: 0.5665 (t80) REVERT: A 190 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7881 (m-10) REVERT: B 31 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8021 (tp) REVERT: B 222 GLN cc_start: 0.7991 (pm20) cc_final: 0.7530 (pm20) REVERT: C 217 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8062 (mm) REVERT: D 99 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7239 (tm-30) REVERT: D 282 ASP cc_start: 0.8691 (t70) cc_final: 0.8437 (t0) REVERT: D 316 ILE cc_start: 0.8264 (mt) cc_final: 0.7986 (tp) REVERT: D 436 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7516 (mp) REVERT: E 19 CYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8776 (t) REVERT: E 41 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.6781 (t70) REVERT: E 199 CYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8113 (m) REVERT: E 308 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8944 (mm) REVERT: E 388 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6454 (mtp180) REVERT: G 368 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8378 (pt) REVERT: G 437 PHE cc_start: 0.7992 (t80) cc_final: 0.7725 (t80) REVERT: H 21 ASN cc_start: 0.8730 (t0) cc_final: 0.8502 (t0) REVERT: H 50 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8893 (p) REVERT: H 284 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8867 (mt) REVERT: H 300 ASP cc_start: 0.7967 (t0) cc_final: 0.7171 (p0) REVERT: I 185 PHE cc_start: 0.4206 (OUTLIER) cc_final: 0.2660 (t80) REVERT: J 29 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9067 (tp) REVERT: J 125 HIS cc_start: 0.6700 (OUTLIER) cc_final: 0.5036 (t-90) REVERT: J 159 ASP cc_start: 0.8738 (t0) cc_final: 0.8474 (t0) REVERT: J 190 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.6945 (m-80) REVERT: J 421 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7607 (t80) REVERT: K 168 GLN cc_start: 0.8942 (tt0) cc_final: 0.8605 (tt0) REVERT: K 222 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7585 (pm20) REVERT: L 188 TRP cc_start: 0.7150 (OUTLIER) cc_final: 0.4946 (t-100) REVERT: L 209 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7703 (tmtt) REVERT: L 245 ASN cc_start: 0.8434 (p0) cc_final: 0.8208 (p0) REVERT: P 220 ASP cc_start: 0.6603 (OUTLIER) cc_final: 0.6249 (p0) REVERT: T 144 GLU cc_start: 0.3999 (OUTLIER) cc_final: 0.3462 (pt0) outliers start: 260 outliers final: 228 residues processed: 532 average time/residue: 0.1952 time to fit residues: 175.8758 Evaluate side-chains 551 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 251 poor density : 300 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 127 CYS 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 240 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 44 LEU 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 107 TYR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 223 CYS Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 388 ARG Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain G residue 359 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 408 TRP Chi-restraints excluded: chain G residue 411 ILE Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 305 ARG Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 346 HIS Chi-restraints excluded: chain H residue 371 CYS Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 393 CYS Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 138 HIS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 211 ASP Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 190 PHE Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 211 SER 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 282 ASP Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 222 GLN Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 346 HIS Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 389 THR Chi-restraints excluded: chain K residue 413 CYS Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 209 LYS Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 237 THR Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain P residue 206 ILE Chi-restraints excluded: chain P residue 209 SER Chi-restraints excluded: chain P residue 220 ASP Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 134 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 111 ARG Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 144 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 35 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 chunk 274 optimal weight: 0.9980 chunk 300 optimal weight: 50.0000 chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 108 optimal weight: 0.0050 chunk 168 optimal weight: 3.9990 chunk 163 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 187 optimal weight: 0.5980 overall best weight: 1.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 GLN D 369 GLN E 167 HIS ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.158466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117710 restraints weight = 46963.212| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.09 r_work: 0.3011 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34796 Z= 0.112 Angle : 0.570 11.453 47460 Z= 0.296 Chirality : 0.044 0.225 5240 Planarity : 0.004 0.072 6128 Dihedral : 5.308 70.809 4722 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.21 % Allowed : 29.41 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.12), residues: 4336 helix: 1.49 (0.29), residues: 372 sheet: -0.52 (0.16), residues: 1148 loop : -1.73 (0.11), residues: 2816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 205 TYR 0.018 0.001 TYR B 357 PHE 0.019 0.001 PHE G 311 TRP 0.019 0.001 TRP L 188 HIS 0.007 0.001 HIS G 125 Details of bonding type rmsd covalent geometry : bond 0.00265 (34712) covalent geometry : angle 0.56714 (47292) SS BOND : bond 0.00209 ( 84) SS BOND : angle 1.08592 ( 168) hydrogen bonds : bond 0.03437 ( 862) hydrogen bonds : angle 4.96484 ( 2280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10685.01 seconds wall clock time: 182 minutes 53.52 seconds (10973.52 seconds total)