Starting phenix.real_space_refine on Sat Jun 28 20:46:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xi5_38371/06_2025/8xi5_38371_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xi5_38371/06_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_38371/06_2025/8xi5_38371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xi5_38371/06_2025/8xi5_38371.map" model { file = "/net/cci-nas-00/data/ceres_data/8xi5_38371/06_2025/8xi5_38371_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xi5_38371/06_2025/8xi5_38371_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 18.22, per 1000 atoms: 0.54 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: 7.28 Conformation dependent library (CDL) restraints added in 4.1 seconds 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: 4.65 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: 12.16 Time building geometry restraints manager: 8.82 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: 0.00 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: 0.630 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: 1.310 Check model and map are aligned: 0.220 Set scattering table: 0.330 Process input model: 70.590 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.330 ------------------------------------------------------------------------------- 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 : 6.48 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.001 TRP D 410 HIS 0.027 0.001 HIS A 183 PHE 0.047 0.002 PHE G 421 TYR 0.034 0.002 TYR A 309 ARG 0.018 0.001 ARG K 390 Details of bonding type rmsd hydrogen bonds : bond 0.28045 ( 862) hydrogen bonds : angle 9.60960 ( 2280) SS BOND : bond 0.04777 ( 84) SS BOND : angle 3.71304 ( 168) covalent geometry : bond 0.00453 (34712) covalent geometry : angle 0.81801 (47292) *********************** 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 : 3.704 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: 0.4481 time to fit residues: 266.0375 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 : 3.789 ------------------------------------------------------------------------------- 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 368 optimal weight: 9.9990 chunk 330 optimal weight: 0.9990 chunk 183 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 341 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 395 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 187 ASN 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 223 GLN J 439 HIS K 194 GLN L 119 ASN N 199 GLN R 151 ASN S 116 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.159315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.119365 restraints weight = 47315.369| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.16 r_work: 0.3057 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 34796 Z= 0.210 Angle : 0.656 12.612 47460 Z= 0.346 Chirality : 0.047 0.251 5240 Planarity : 0.006 0.083 6128 Dihedral : 5.862 75.690 4724 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.07 % Allowed : 28.66 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.12), residues: 4336 helix: -1.52 (0.23), residues: 396 sheet: -0.63 (0.16), residues: 1136 loop : -1.99 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 188 HIS 0.013 0.001 HIS A 183 PHE 0.037 0.002 PHE J 311 TYR 0.025 0.002 TYR A 309 ARG 0.004 0.000 ARG B 119 Details of bonding type rmsd hydrogen bonds : bond 0.05293 ( 862) hydrogen bonds : angle 6.12319 ( 2280) SS BOND : bond 0.00358 ( 84) SS BOND : angle 1.14336 ( 168) covalent geometry : bond 0.00507 (34712) covalent geometry : angle 0.65333 (47292) *********************** 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 521 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 331 time to evaluate : 3.666 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: 0.9306 (ptm) cc_final: 0.8976 (ptm) REVERT: B 357 TYR cc_start: 0.8955 (t80) cc_final: 0.8747 (t80) REVERT: B 384 TRP cc_start: 0.7132 (t60) cc_final: 0.6914 (t-100) REVERT: B 398 LYS cc_start: 0.8113 (tttm) cc_final: 0.7891 (tttm) REVERT: C 121 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.7076 (pm20) REVERT: C 217 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7961 (mm) REVERT: D 434 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6793 (mp) REVERT: E 41 HIS cc_start: 0.9064 (OUTLIER) cc_final: 0.7257 (t70) REVERT: E 199 CYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8249 (m) REVERT: E 292 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9153 (tt) REVERT: E 362 LEU cc_start: 0.8651 (mm) cc_final: 0.8354 (tp) REVERT: F 170 MET cc_start: 0.4251 (pmm) cc_final: 0.3961 (pmm) REVERT: G 368 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8684 (pt) REVERT: H 68 MET cc_start: 0.8392 (ptm) cc_final: 0.8161 (ptp) REVERT: J 45 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8099 (mt-10) REVERT: J 125 HIS cc_start: 0.6890 (OUTLIER) cc_final: 0.5587 (t-90) REVERT: J 192 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7865 (tp30) REVERT: J 328 ASN cc_start: 0.8726 (m110) cc_final: 0.8224 (t0) REVERT: J 370 VAL cc_start: 0.9318 (OUTLIER) cc_final: 0.9075 (p) REVERT: J 438 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8595 (m-80) REVERT: L 186 TYR cc_start: 0.7548 (m-80) cc_final: 0.7215 (m-80) REVERT: L 195 TYR cc_start: 0.5154 (t80) cc_final: 0.4763 (t80) REVERT: S 111 ARG cc_start: 0.4078 (OUTLIER) cc_final: 0.3132 (tpt170) outliers start: 190 outliers final: 122 residues processed: 493 average time/residue: 0.4418 time to fit residues: 367.3539 Evaluate side-chains 449 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 316 time to evaluate : 3.806 ------------------------------------------------------------------------------- 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 172 VAL Chi-restraints excluded: chain B residue 199 CYS 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 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 292 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 157 ILE Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 185 VAL 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 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 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 133 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 145 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 291 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 369 optimal weight: 0.5980 chunk 312 optimal weight: 9.9990 chunk 320 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 397 optimal weight: 30.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- 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 E 155 HIS E 168 GLN E 222 GLN ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 332 HIS ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 GLN ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 HIS K 94 HIS K 194 GLN K 253 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.156975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116959 restraints weight = 47758.426| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.19 r_work: 0.2985 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 34796 Z= 0.224 Angle : 0.654 11.030 47460 Z= 0.343 Chirality : 0.047 0.211 5240 Planarity : 0.005 0.068 6128 Dihedral : 5.892 74.923 4724 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 7.05 % Allowed : 27.40 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.12), residues: 4336 helix: -0.07 (0.27), residues: 372 sheet: -0.73 (0.15), residues: 1216 loop : -1.92 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 188 HIS 0.006 0.001 HIS G 125 PHE 0.042 0.002 PHE J 311 TYR 0.026 0.002 TYR A 309 ARG 0.006 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 862) hydrogen bonds : angle 5.68672 ( 2280) SS BOND : bond 0.00392 ( 84) SS BOND : angle 1.21738 ( 168) covalent geometry : bond 0.00546 (34712) covalent geometry : angle 0.65103 (47292) *********************** 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 593 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 329 time to evaluate : 3.854 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: B 221 LYS cc_start: 0.8965 (mtmm) cc_final: 0.8753 (mtmm) REVERT: B 280 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8847 (tp) REVERT: B 384 TRP cc_start: 0.7205 (t60) cc_final: 0.6860 (t-100) REVERT: C 217 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7899 (mm) REVERT: D 67 GLN cc_start: 0.8721 (mp10) cc_final: 0.8432 (mp10) REVERT: D 99 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7229 (tm-30) REVERT: D 282 ASP cc_start: 0.8842 (t70) cc_final: 0.8535 (t0) REVERT: D 316 ILE cc_start: 0.8404 (mt) cc_final: 0.8106 (tp) REVERT: D 369 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8771 (pt0) REVERT: E 19 CYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8704 (t) REVERT: E 41 HIS cc_start: 0.9126 (OUTLIER) cc_final: 0.7179 (t70) REVERT: E 199 CYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8056 (m) REVERT: E 308 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.9027 (mm) REVERT: E 399 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7296 (mt) REVERT: F 188 TRP cc_start: 0.6894 (t-100) cc_final: 0.6582 (t-100) REVERT: G 368 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8615 (pt) REVERT: H 284 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8872 (mt) REVERT: I 185 PHE cc_start: 0.4383 (OUTLIER) cc_final: 0.3687 (t80) REVERT: J 29 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9039 (tp) REVERT: J 125 HIS cc_start: 0.6885 (OUTLIER) cc_final: 0.5207 (t-90) REVERT: J 328 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8349 (t0) REVERT: J 370 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8985 (p) REVERT: J 438 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8501 (m-10) REVERT: K 222 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: L 186 TYR cc_start: 0.7643 (m-80) cc_final: 0.7323 (m-80) REVERT: L 195 TYR cc_start: 0.5195 (t80) cc_final: 0.4768 (t80) REVERT: L 209 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7514 (tmtt) outliers start: 264 outliers final: 182 residues processed: 549 average time/residue: 0.4202 time to fit residues: 383.6674 Evaluate side-chains 519 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 319 time to evaluate : 3.895 ------------------------------------------------------------------------------- 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 101 THR 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 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 408 TRP 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 44 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL 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 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 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 C residue 128 VAL 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 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 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 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 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 44 VAL 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 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 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 399 LEU 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 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 162 LEU 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 232 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 339 VAL 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 411 ILE Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 ASP 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 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 412 LEU 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 53 THR 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 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 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 328 ASN 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 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 41 HIS Chi-restraints excluded: chain K residue 72 THR 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 361 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 318 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 380 optimal weight: 6.9990 chunk 382 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 110 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 361 ASN D 369 GLN E 222 GLN E 358 ASN G 30 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS J 100 ASN J 439 HIS K 41 HIS ** K 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN ** N 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.157663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.118413 restraints weight = 47454.923| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.26 r_work: 0.2985 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34796 Z= 0.108 Angle : 0.564 11.300 47460 Z= 0.295 Chirality : 0.044 0.193 5240 Planarity : 0.004 0.062 6128 Dihedral : 5.480 73.008 4724 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.02 % Allowed : 29.25 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.12), residues: 4336 helix: 0.60 (0.28), residues: 372 sheet: -0.61 (0.15), residues: 1160 loop : -1.82 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 188 HIS 0.016 0.001 HIS K 41 PHE 0.018 0.001 PHE G 311 TYR 0.018 0.001 TYR A 309 ARG 0.006 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 862) hydrogen bonds : angle 5.27902 ( 2280) SS BOND : bond 0.00290 ( 84) SS BOND : angle 0.98867 ( 168) covalent geometry : bond 0.00253 (34712) covalent geometry : angle 0.56215 (47292) *********************** 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 524 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 336 time to evaluate : 3.721 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 316 ILE cc_start: 0.8704 (mt) cc_final: 0.8334 (tp) REVERT: B 200 LYS cc_start: 0.8185 (tppp) cc_final: 0.7895 (ttmt) REVERT: B 398 LYS cc_start: 0.8173 (tttm) cc_final: 0.7961 (tttm) REVERT: D 99 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7207 (tm-30) REVERT: D 282 ASP cc_start: 0.8760 (t70) cc_final: 0.8470 (t0) REVERT: D 316 ILE cc_start: 0.8288 (mt) cc_final: 0.8011 (tp) REVERT: D 436 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7438 (mp) REVERT: E 41 HIS cc_start: 0.8997 (OUTLIER) cc_final: 0.6757 (t70) REVERT: E 199 CYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8070 (m) REVERT: E 399 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7337 (mt) REVERT: G 368 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8514 (pt) REVERT: H 50 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8931 (p) REVERT: H 74 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8181 (mtpp) REVERT: H 284 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8835 (mt) REVERT: H 300 ASP cc_start: 0.8015 (t0) cc_final: 0.7134 (p0) REVERT: I 185 PHE cc_start: 0.4345 (OUTLIER) cc_final: 0.3629 (t80) REVERT: J 45 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8080 (mm-30) REVERT: J 125 HIS cc_start: 0.6587 (OUTLIER) cc_final: 0.5054 (t-90) REVERT: J 344 ASP cc_start: 0.8971 (p0) cc_final: 0.8694 (p0) REVERT: J 370 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8835 (p) REVERT: J 438 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: K 222 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7440 (pm20) REVERT: L 186 TYR cc_start: 0.7448 (m-80) cc_final: 0.7231 (m-80) REVERT: L 209 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7335 (tmtt) REVERT: L 245 ASN cc_start: 0.8598 (p0) cc_final: 0.8195 (p0) REVERT: S 111 ARG cc_start: 0.4096 (OUTLIER) cc_final: 0.3040 (tpt170) REVERT: S 137 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5756 (pm20) outliers start: 188 outliers final: 127 residues processed: 498 average time/residue: 0.4467 time to fit residues: 373.0861 Evaluate side-chains 463 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 320 time to evaluate : 4.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 208 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 354 THR 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 128 VAL Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 240 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 230 VAL 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 408 TRP Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 436 LEU 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 143 GLU Chi-restraints excluded: chain E residue 199 CYS 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 399 LEU Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 202 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 157 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 319 VAL 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 411 ILE 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 24 HIS Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 178 LEU 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 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 202 VAL Chi-restraints excluded: chain I residue 242 VAL 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 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 232 THR Chi-restraints excluded: chain J residue 253 ASN Chi-restraints excluded: chain J residue 282 ASP Chi-restraints excluded: chain J residue 319 VAL 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 J residue 438 PHE 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 124 VAL Chi-restraints excluded: chain K residue 128 VAL 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 313 THR Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 389 THR 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 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 Q residue 134 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 355 optimal weight: 1.9990 chunk 368 optimal weight: 0.8980 chunk 231 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 425 optimal weight: 50.0000 chunk 229 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 332 optimal weight: 10.0000 chunk 430 optimal weight: 40.0000 chunk 74 optimal weight: 0.3980 chunk 384 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 439 HIS K 155 HIS ** N 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.160550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.120701 restraints weight = 47518.205| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.23 r_work: 0.2980 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34796 Z= 0.122 Angle : 0.564 10.515 47460 Z= 0.294 Chirality : 0.044 0.188 5240 Planarity : 0.004 0.056 6128 Dihedral : 5.314 71.568 4722 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 5.82 % Allowed : 28.31 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.12), residues: 4336 helix: 0.99 (0.28), residues: 372 sheet: -0.56 (0.15), residues: 1172 loop : -1.75 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 188 HIS 0.013 0.001 HIS J 439 PHE 0.023 0.001 PHE J 311 TYR 0.018 0.001 TYR A 309 ARG 0.006 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 862) hydrogen bonds : angle 5.11257 ( 2280) SS BOND : bond 0.00269 ( 84) SS BOND : angle 1.08531 ( 168) covalent geometry : bond 0.00293 (34712) covalent geometry : angle 0.56100 (47292) *********************** 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 542 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 324 time to evaluate : 3.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 217 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7865 (mm) REVERT: D 99 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7225 (tm-30) REVERT: D 282 ASP cc_start: 0.8761 (t70) cc_final: 0.8470 (t0) REVERT: D 316 ILE cc_start: 0.8295 (mt) cc_final: 0.8028 (tp) REVERT: D 410 TRP cc_start: 0.8261 (m100) cc_final: 0.7687 (m100) REVERT: D 436 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7417 (mp) REVERT: E 19 CYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8731 (t) REVERT: E 41 HIS cc_start: 0.8990 (OUTLIER) cc_final: 0.6764 (t70) REVERT: E 199 CYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8142 (m) REVERT: E 388 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6562 (mtp180) REVERT: G 368 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8377 (pt) REVERT: H 27 CYS cc_start: 0.7854 (m) cc_final: 0.7441 (p) REVERT: H 50 SER cc_start: 0.9172 (OUTLIER) cc_final: 0.8921 (p) REVERT: H 284 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8839 (mt) REVERT: H 300 ASP cc_start: 0.8024 (t0) cc_final: 0.7168 (p0) REVERT: H 305 ARG cc_start: 0.9378 (OUTLIER) cc_final: 0.9155 (ptm-80) REVERT: I 185 PHE cc_start: 0.4551 (OUTLIER) cc_final: 0.3794 (t80) REVERT: J 344 ASP cc_start: 0.8963 (p0) cc_final: 0.8687 (p0) REVERT: J 370 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8859 (p) REVERT: J 421 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7411 (t80) REVERT: J 438 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: K 168 GLN cc_start: 0.8934 (tt0) cc_final: 0.8639 (tt0) REVERT: K 222 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7397 (pm20) REVERT: L 186 TYR cc_start: 0.7458 (m-80) cc_final: 0.7194 (m-80) REVERT: L 195 TYR cc_start: 0.5292 (t80) cc_final: 0.4733 (t80) REVERT: L 209 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7416 (tmtt) REVERT: L 245 ASN cc_start: 0.8534 (p0) cc_final: 0.8218 (p0) REVERT: S 111 ARG cc_start: 0.4344 (OUTLIER) cc_final: 0.3158 (tpt170) REVERT: S 137 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.5753 (pm20) outliers start: 218 outliers final: 161 residues processed: 511 average time/residue: 0.4525 time to fit residues: 389.4458 Evaluate side-chains 493 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 314 time to evaluate : 4.081 ------------------------------------------------------------------------------- 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 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 208 THR 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 378 LYS Chi-restraints excluded: chain A residue 418 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 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 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 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 C residue 158 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain D residue 19 VAL 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 230 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 296 THR 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 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 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 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 223 CYS Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 388 ARG Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 405 VAL 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 G residue 6 VAL 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 157 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL 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 396 THR Chi-restraints excluded: chain G residue 411 ILE Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 438 PHE Chi-restraints excluded: chain H residue 24 HIS Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 133 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 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 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 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 124 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 185 VAL 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 318 THR Chi-restraints excluded: chain J residue 319 VAL 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 J residue 438 PHE 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 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 314 VAL Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 389 THR 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 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 209 SER 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 S residue 137 GLU 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 141 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 329 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 254 optimal weight: 1.9990 chunk 331 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 257 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 30 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 439 HIS K 155 HIS K 194 GLN ** N 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.158038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.117978 restraints weight = 47452.277| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.17 r_work: 0.2948 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 34796 Z= 0.202 Angle : 0.624 9.689 47460 Z= 0.325 Chirality : 0.046 0.192 5240 Planarity : 0.005 0.060 6128 Dihedral : 5.551 71.143 4722 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 6.97 % Allowed : 27.48 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.12), residues: 4336 helix: 1.07 (0.28), residues: 372 sheet: -0.61 (0.15), residues: 1192 loop : -1.78 (0.11), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 188 HIS 0.018 0.001 HIS J 439 PHE 0.038 0.002 PHE J 311 TYR 0.024 0.002 TYR A 309 ARG 0.006 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 862) hydrogen bonds : angle 5.18604 ( 2280) SS BOND : bond 0.00335 ( 84) SS BOND : angle 1.32247 ( 168) covalent geometry : bond 0.00496 (34712) covalent geometry : angle 0.61988 (47292) *********************** 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 573 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 261 poor density : 312 time to evaluate : 4.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.7990 (tp) REVERT: B 280 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8864 (tt) REVERT: C 217 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7953 (mm) REVERT: D 67 GLN cc_start: 0.8806 (mp10) cc_final: 0.8559 (mp10) REVERT: D 99 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7250 (tm-30) REVERT: D 282 ASP cc_start: 0.8779 (t70) cc_final: 0.8476 (t0) REVERT: D 316 ILE cc_start: 0.8330 (mt) cc_final: 0.8045 (tp) REVERT: D 436 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7586 (mp) REVERT: E 19 CYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8676 (t) REVERT: E 41 HIS cc_start: 0.9079 (OUTLIER) cc_final: 0.6993 (t70) REVERT: E 199 CYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8133 (m) REVERT: E 308 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8980 (mm) REVERT: E 388 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6351 (mtp180) REVERT: G 368 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8491 (pt) REVERT: H 50 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8918 (p) REVERT: H 284 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8856 (mt) REVERT: H 300 ASP cc_start: 0.8052 (t0) cc_final: 0.7241 (p0) REVERT: I 185 PHE cc_start: 0.3730 (OUTLIER) cc_final: 0.2419 (t80) REVERT: J 29 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9105 (tt) REVERT: J 103 MET cc_start: 0.8115 (mtp) cc_final: 0.7902 (ttm) REVERT: J 125 HIS cc_start: 0.6783 (OUTLIER) cc_final: 0.5109 (t-90) REVERT: J 328 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8376 (t0) REVERT: J 370 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8963 (p) REVERT: J 395 HIS cc_start: 0.9219 (OUTLIER) cc_final: 0.8995 (p90) REVERT: J 421 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7217 (t80) REVERT: J 438 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8287 (m-80) REVERT: K 168 GLN cc_start: 0.8939 (tt0) cc_final: 0.8613 (tt0) REVERT: K 222 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: L 186 TYR cc_start: 0.7759 (m-80) cc_final: 0.7404 (m-80) REVERT: L 188 TRP cc_start: 0.7136 (OUTLIER) cc_final: 0.4778 (t-100) REVERT: L 195 TYR cc_start: 0.5511 (t80) cc_final: 0.4908 (t80) REVERT: L 209 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7648 (tmtt) REVERT: L 245 ASN cc_start: 0.8502 (p0) cc_final: 0.8247 (p0) REVERT: S 111 ARG cc_start: 0.4369 (OUTLIER) cc_final: 0.3186 (tpt170) outliers start: 261 outliers final: 200 residues processed: 538 average time/residue: 0.4716 time to fit residues: 427.3234 Evaluate side-chains 527 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 303 time to evaluate : 3.966 ------------------------------------------------------------------------------- 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 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 362 ILE 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 A residue 418 THR 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 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 280 LEU 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 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 135 ILE 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 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 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 308 ILE Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 388 ARG 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 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 162 LEU 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 235 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 319 VAL 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 411 ILE Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 438 PHE Chi-restraints excluded: chain H residue 24 HIS 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 172 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 185 VAL 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 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 H residue 414 CYS 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 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 55 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 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 281 ILE 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 328 ASN 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 370 VAL Chi-restraints excluded: chain J residue 395 HIS 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 438 PHE 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 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 188 TRP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 139 optimal weight: 7.9990 chunk 196 optimal weight: 0.3980 chunk 383 optimal weight: 8.9990 chunk 232 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 386 optimal weight: 1.9990 chunk 381 optimal weight: 0.0370 chunk 150 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 162 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 overall best weight: 1.6864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN G 30 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 HIS ** N 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.158092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.118612 restraints weight = 47645.630| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.22 r_work: 0.2990 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34796 Z= 0.110 Angle : 0.565 9.770 47460 Z= 0.294 Chirality : 0.044 0.189 5240 Planarity : 0.004 0.070 6128 Dihedral : 5.287 69.810 4722 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 5.50 % Allowed : 28.87 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.12), residues: 4336 helix: 1.34 (0.28), residues: 372 sheet: -0.54 (0.15), residues: 1172 loop : -1.71 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 210 HIS 0.012 0.001 HIS J 439 PHE 0.019 0.001 PHE G 311 TYR 0.018 0.001 TYR A 309 ARG 0.007 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 862) hydrogen bonds : angle 4.99021 ( 2280) SS BOND : bond 0.00219 ( 84) SS BOND : angle 1.07124 ( 168) covalent geometry : bond 0.00261 (34712) covalent geometry : angle 0.56206 (47292) *********************** 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 527 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 321 time to evaluate : 4.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.7959 (tp) REVERT: C 181 LYS cc_start: 0.3713 (OUTLIER) cc_final: 0.3492 (ptpp) REVERT: C 217 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7944 (mm) REVERT: D 67 GLN cc_start: 0.8750 (mp10) cc_final: 0.8493 (mp10) REVERT: D 99 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7225 (tm-30) REVERT: D 282 ASP cc_start: 0.8682 (t70) cc_final: 0.8409 (t0) REVERT: D 316 ILE cc_start: 0.8274 (mt) cc_final: 0.8018 (tp) REVERT: D 436 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7566 (mp) REVERT: E 19 CYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8730 (t) REVERT: E 41 HIS cc_start: 0.8977 (OUTLIER) cc_final: 0.6754 (t70) REVERT: E 199 CYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8096 (m) REVERT: E 388 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6025 (mtp180) REVERT: G 368 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8409 (pt) REVERT: H 50 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8914 (p) REVERT: H 284 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8838 (mt) REVERT: H 300 ASP cc_start: 0.8031 (t0) cc_final: 0.7194 (p0) REVERT: I 185 PHE cc_start: 0.3755 (OUTLIER) cc_final: 0.2409 (t80) REVERT: J 99 GLU cc_start: 0.7894 (pp20) cc_final: 0.7692 (pp20) REVERT: J 103 MET cc_start: 0.8156 (mtp) cc_final: 0.7923 (ttm) REVERT: J 125 HIS cc_start: 0.6466 (OUTLIER) cc_final: 0.4901 (t-90) REVERT: J 344 ASP cc_start: 0.8946 (p0) cc_final: 0.8690 (p0) REVERT: J 370 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8832 (p) REVERT: J 421 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7322 (t80) REVERT: K 168 GLN cc_start: 0.8917 (tt0) cc_final: 0.8615 (tt0) REVERT: K 222 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: L 186 TYR cc_start: 0.7465 (m-80) cc_final: 0.7241 (m-80) REVERT: L 195 TYR cc_start: 0.5479 (t80) cc_final: 0.4857 (t80) REVERT: L 209 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7459 (tmtt) REVERT: L 245 ASN cc_start: 0.8483 (p0) cc_final: 0.8198 (p0) REVERT: S 137 GLU cc_start: 0.6271 (OUTLIER) cc_final: 0.5872 (pm20) outliers start: 206 outliers final: 169 residues processed: 500 average time/residue: 0.4384 time to fit residues: 366.6848 Evaluate side-chains 499 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 312 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE 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 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 195 THR Chi-restraints excluded: chain A residue 208 THR 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 418 THR 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 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 247 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 181 LYS 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 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 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 319 VAL Chi-restraints excluded: chain D residue 359 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 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 172 VAL Chi-restraints excluded: chain E residue 199 CYS 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 321 GLU Chi-restraints excluded: chain E residue 388 ARG 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 G residue 29 LEU 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 157 ILE Chi-restraints excluded: chain G residue 162 LEU 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 235 THR 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 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 434 LEU Chi-restraints excluded: chain G residue 438 PHE 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 164 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 LEU 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 418 THR 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 82 SER Chi-restraints excluded: chain J residue 107 TYR 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 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 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 389 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 438 PHE Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS 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 314 VAL Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 389 THR 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 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 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 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 59 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 39 optimal weight: 0.0270 chunk 305 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 424 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 215 optimal weight: 20.0000 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN D 32 GLN G 30 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 439 HIS K 155 HIS ** N 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.158571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119234 restraints weight = 47242.488| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.23 r_work: 0.3065 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34796 Z= 0.115 Angle : 0.559 9.670 47460 Z= 0.290 Chirality : 0.044 0.200 5240 Planarity : 0.004 0.062 6128 Dihedral : 5.194 68.588 4722 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 5.98 % Allowed : 28.15 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.12), residues: 4336 helix: 1.50 (0.28), residues: 372 sheet: -0.48 (0.15), residues: 1164 loop : -1.69 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 188 HIS 0.007 0.001 HIS G 125 PHE 0.024 0.001 PHE H 248 TYR 0.018 0.001 TYR A 309 ARG 0.007 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 862) hydrogen bonds : angle 4.91138 ( 2280) SS BOND : bond 0.00221 ( 84) SS BOND : angle 1.08872 ( 168) covalent geometry : bond 0.00276 (34712) covalent geometry : angle 0.55630 (47292) *********************** 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 537 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 313 time to evaluate : 4.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8009 (tp) REVERT: B 222 GLN cc_start: 0.7965 (pm20) cc_final: 0.7709 (pm20) REVERT: C 217 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7948 (mm) REVERT: D 67 GLN cc_start: 0.8755 (mp10) cc_final: 0.8513 (mp10) REVERT: D 99 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7334 (tm-30) REVERT: D 282 ASP cc_start: 0.8746 (t70) cc_final: 0.8478 (t0) REVERT: D 316 ILE cc_start: 0.8378 (mt) cc_final: 0.8160 (tp) REVERT: D 436 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7612 (mp) REVERT: E 19 CYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8740 (t) REVERT: E 41 HIS cc_start: 0.8944 (OUTLIER) cc_final: 0.6779 (t70) REVERT: E 199 CYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8391 (m) REVERT: E 308 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8935 (mm) REVERT: E 388 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.6215 (mtp180) REVERT: G 368 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8566 (pt) REVERT: G 437 PHE cc_start: 0.8118 (t80) cc_final: 0.7891 (t80) REVERT: H 50 SER cc_start: 0.9181 (OUTLIER) cc_final: 0.8938 (p) REVERT: H 74 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8210 (mtpp) REVERT: H 284 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8887 (mt) REVERT: H 300 ASP cc_start: 0.8134 (t0) cc_final: 0.7355 (p0) REVERT: I 185 PHE cc_start: 0.3775 (OUTLIER) cc_final: 0.2316 (t80) REVERT: J 29 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9052 (tp) REVERT: J 99 GLU cc_start: 0.7861 (pp20) cc_final: 0.7581 (tm-30) REVERT: J 103 MET cc_start: 0.8260 (mtp) cc_final: 0.8013 (ttm) REVERT: J 125 HIS cc_start: 0.6551 (OUTLIER) cc_final: 0.5024 (t-90) REVERT: J 344 ASP cc_start: 0.8928 (p0) cc_final: 0.8678 (p0) REVERT: J 370 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8833 (p) REVERT: J 421 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7365 (t80) REVERT: K 168 GLN cc_start: 0.8870 (tt0) cc_final: 0.8578 (tt0) REVERT: K 222 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: L 186 TYR cc_start: 0.7524 (m-80) cc_final: 0.7293 (m-80) REVERT: L 188 TRP cc_start: 0.7022 (OUTLIER) cc_final: 0.4833 (t-100) REVERT: L 209 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7462 (tmtt) REVERT: L 245 ASN cc_start: 0.8464 (p0) cc_final: 0.8219 (p0) REVERT: S 137 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5870 (pm20) outliers start: 224 outliers final: 182 residues processed: 508 average time/residue: 0.4262 time to fit residues: 363.8900 Evaluate side-chains 512 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 309 time to evaluate : 4.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE 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 124 VAL Chi-restraints excluded: chain A residue 156 LYS 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 354 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 418 THR 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 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 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 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 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 47 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 116 ILE 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 319 VAL Chi-restraints excluded: chain D residue 359 THR 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 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 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 395 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 239 LEU 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 157 ILE Chi-restraints excluded: chain G residue 162 LEU 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 235 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 319 VAL 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 434 LEU Chi-restraints excluded: chain G residue 438 PHE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 133 VAL 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 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 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 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 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 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 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 354 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 389 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 438 PHE 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 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 365 ILE Chi-restraints excluded: chain K residue 371 CYS 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 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 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 137 GLU Chi-restraints excluded: chain T residue 130 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 97 optimal weight: 30.0000 chunk 353 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 314 optimal weight: 5.9990 chunk 68 optimal weight: 0.0010 chunk 207 optimal weight: 10.0000 chunk 289 optimal weight: 7.9990 chunk 293 optimal weight: 1.9990 chunk 375 optimal weight: 6.9990 chunk 269 optimal weight: 2.9990 overall best weight: 3.5994 ------------------------------------------------------------------------------- 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 G 30 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 439 HIS K 155 HIS ** N 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.157088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117506 restraints weight = 47600.452| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.23 r_work: 0.3045 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34796 Z= 0.162 Angle : 0.592 10.298 47460 Z= 0.307 Chirality : 0.045 0.188 5240 Planarity : 0.004 0.061 6128 Dihedral : 5.320 68.739 4722 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 6.17 % Allowed : 28.21 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.12), residues: 4336 helix: 1.49 (0.28), residues: 372 sheet: -0.54 (0.15), residues: 1164 loop : -1.71 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 210 HIS 0.007 0.001 HIS G 125 PHE 0.031 0.001 PHE J 311 TYR 0.021 0.001 TYR A 309 ARG 0.007 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 862) hydrogen bonds : angle 4.96455 ( 2280) SS BOND : bond 0.00263 ( 84) SS BOND : angle 1.17939 ( 168) covalent geometry : bond 0.00395 (34712) covalent geometry : angle 0.58864 (47292) *********************** 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 543 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 312 time to evaluate : 4.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7882 (m-10) REVERT: B 31 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8013 (tp) REVERT: B 222 GLN cc_start: 0.8300 (pm20) cc_final: 0.7875 (pm20) REVERT: C 217 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7978 (mm) REVERT: D 67 GLN cc_start: 0.8790 (mp10) cc_final: 0.8569 (mp10) REVERT: D 99 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7323 (tm-30) REVERT: D 282 ASP cc_start: 0.8800 (t70) cc_final: 0.8516 (t0) REVERT: D 316 ILE cc_start: 0.8391 (mt) cc_final: 0.8155 (tp) REVERT: D 436 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7598 (mp) REVERT: E 19 CYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8693 (t) REVERT: E 41 HIS cc_start: 0.8969 (OUTLIER) cc_final: 0.6828 (t70) REVERT: E 199 CYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8417 (m) REVERT: E 308 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8965 (mm) REVERT: E 388 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.6226 (mtp180) REVERT: G 311 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6191 (p90) REVERT: G 342 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: G 368 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8519 (pt) REVERT: G 437 PHE cc_start: 0.8111 (t80) cc_final: 0.7884 (t80) REVERT: H 50 SER cc_start: 0.9164 (OUTLIER) cc_final: 0.8920 (p) REVERT: H 284 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8885 (mt) REVERT: H 300 ASP cc_start: 0.8092 (t0) cc_final: 0.7328 (p0) REVERT: I 185 PHE cc_start: 0.3859 (OUTLIER) cc_final: 0.2362 (t80) REVERT: J 29 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9089 (tt) REVERT: J 99 GLU cc_start: 0.7945 (pp20) cc_final: 0.7638 (tm-30) REVERT: J 103 MET cc_start: 0.8181 (mtp) cc_final: 0.7964 (ttm) REVERT: J 125 HIS cc_start: 0.6761 (OUTLIER) cc_final: 0.5156 (t-90) REVERT: J 344 ASP cc_start: 0.8947 (p0) cc_final: 0.8683 (p0) REVERT: J 370 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8894 (p) REVERT: J 421 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7320 (t80) REVERT: J 438 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: K 168 GLN cc_start: 0.8894 (tt0) cc_final: 0.8589 (tt0) REVERT: K 222 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7733 (pm20) REVERT: L 186 TYR cc_start: 0.7634 (m-80) cc_final: 0.7367 (m-80) REVERT: L 188 TRP cc_start: 0.7186 (OUTLIER) cc_final: 0.4851 (t-100) REVERT: L 209 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7542 (tmtt) REVERT: L 245 ASN cc_start: 0.8468 (p0) cc_final: 0.8231 (p0) REVERT: S 137 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.5847 (pm20) outliers start: 231 outliers final: 199 residues processed: 513 average time/residue: 0.3993 time to fit residues: 344.4083 Evaluate side-chains 530 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 307 time to evaluate : 3.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE 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 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 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 A residue 418 THR 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 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 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 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 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 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 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 319 VAL Chi-restraints excluded: chain D residue 359 THR 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 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 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 157 ILE Chi-restraints excluded: chain G residue 162 LEU 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 235 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 311 PHE Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 342 GLU 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 434 LEU Chi-restraints excluded: chain G residue 435 VAL Chi-restraints excluded: chain G residue 438 PHE Chi-restraints excluded: chain H residue 28 ASP 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 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 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 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 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 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 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 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 354 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 389 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 438 PHE 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 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 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 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 S residue 137 GLU Chi-restraints excluded: chain T residue 130 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 69 optimal weight: 0.5980 chunk 187 optimal weight: 5.9990 chunk 416 optimal weight: 6.9990 chunk 369 optimal weight: 8.9990 chunk 396 optimal weight: 0.8980 chunk 203 optimal weight: 10.0000 chunk 399 optimal weight: 9.9990 chunk 360 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 387 optimal weight: 0.0050 overall best weight: 2.8998 ------------------------------------------------------------------------------- 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 ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 HIS ** N 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.157496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117808 restraints weight = 47210.154| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.16 r_work: 0.3060 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34796 Z= 0.140 Angle : 0.581 11.740 47460 Z= 0.302 Chirality : 0.045 0.219 5240 Planarity : 0.004 0.062 6128 Dihedral : 5.294 68.529 4722 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 6.30 % Allowed : 28.02 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.12), residues: 4336 helix: 1.55 (0.29), residues: 372 sheet: -0.54 (0.15), residues: 1164 loop : -1.70 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 188 HIS 0.007 0.001 HIS G 125 PHE 0.026 0.001 PHE J 311 TYR 0.021 0.001 TYR B 357 ARG 0.007 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 862) hydrogen bonds : angle 4.94380 ( 2280) SS BOND : bond 0.00241 ( 84) SS BOND : angle 1.08726 ( 168) covalent geometry : bond 0.00340 (34712) covalent geometry : angle 0.57847 (47292) ********************** 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 536 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 300 time to evaluate : 4.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8027 (tp) REVERT: B 222 GLN cc_start: 0.8310 (pm20) cc_final: 0.7909 (pm20) REVERT: C 217 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.8005 (mm) REVERT: D 67 GLN cc_start: 0.8783 (mp10) cc_final: 0.8570 (mp10) REVERT: D 99 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7370 (tm-30) REVERT: D 282 ASP cc_start: 0.8750 (t70) cc_final: 0.8480 (t0) REVERT: D 316 ILE cc_start: 0.8418 (mt) cc_final: 0.8205 (tp) REVERT: D 436 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7583 (mp) REVERT: E 19 CYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8694 (t) REVERT: E 41 HIS cc_start: 0.8945 (OUTLIER) cc_final: 0.6845 (t70) REVERT: E 199 CYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8399 (m) REVERT: E 308 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8953 (mm) REVERT: E 388 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.6238 (mtp180) REVERT: G 311 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6198 (p90) REVERT: G 368 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8536 (pt) REVERT: H 50 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8914 (p) REVERT: H 74 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8227 (mtpp) REVERT: H 284 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8893 (mt) REVERT: H 300 ASP cc_start: 0.8099 (t0) cc_final: 0.7366 (p0) REVERT: I 185 PHE cc_start: 0.4040 (OUTLIER) cc_final: 0.2575 (t80) REVERT: J 29 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9089 (tt) REVERT: J 99 GLU cc_start: 0.7927 (pp20) cc_final: 0.7631 (tm-30) REVERT: J 103 MET cc_start: 0.8149 (mtp) cc_final: 0.7916 (ttm) REVERT: J 125 HIS cc_start: 0.6813 (OUTLIER) cc_final: 0.5201 (t-90) REVERT: J 344 ASP cc_start: 0.8916 (p0) cc_final: 0.8663 (p0) REVERT: J 370 VAL cc_start: 0.9085 (OUTLIER) cc_final: 0.8881 (p) REVERT: J 421 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7362 (t80) REVERT: J 438 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: K 168 GLN cc_start: 0.8893 (tt0) cc_final: 0.8602 (tt0) REVERT: K 222 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7720 (pm20) REVERT: L 186 TYR cc_start: 0.7635 (m-80) cc_final: 0.7227 (m-80) REVERT: L 188 TRP cc_start: 0.7199 (OUTLIER) cc_final: 0.4857 (t-100) REVERT: L 209 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7528 (tmtt) REVERT: L 245 ASN cc_start: 0.8467 (p0) cc_final: 0.8235 (p0) REVERT: S 137 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.5973 (pm20) outliers start: 236 outliers final: 201 residues processed: 506 average time/residue: 0.4979 time to fit residues: 431.3658 Evaluate side-chains 521 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 297 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE 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 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 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 322 LYS 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 A residue 418 THR 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 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 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 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 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 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 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 319 VAL Chi-restraints excluded: chain D residue 359 THR 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 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 G residue 7 MET Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 75 ASP 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 235 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 311 PHE Chi-restraints excluded: chain G residue 319 VAL 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 434 LEU Chi-restraints excluded: chain G residue 435 VAL Chi-restraints excluded: chain G residue 438 PHE Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 65 MET Chi-restraints excluded: chain H residue 74 LYS 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 164 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 LEU 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 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 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 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 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 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 354 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 389 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 438 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 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 314 VAL Chi-restraints excluded: chain K residue 346 HIS Chi-restraints excluded: chain K residue 371 CYS 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 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 S residue 137 GLU Chi-restraints excluded: chain T residue 130 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 310 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 chunk 414 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 399 optimal weight: 8.9990 chunk 270 optimal weight: 0.5980 chunk 390 optimal weight: 0.5980 chunk 372 optimal weight: 4.9990 chunk 344 optimal weight: 2.9990 chunk 358 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- 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 G 30 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 HIS ** N 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.157923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118011 restraints weight = 47150.238| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.22 r_work: 0.3006 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34796 Z= 0.145 Angle : 0.583 11.221 47460 Z= 0.303 Chirality : 0.045 0.212 5240 Planarity : 0.004 0.062 6128 Dihedral : 5.289 68.315 4722 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 6.36 % Allowed : 27.88 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.12), residues: 4336 helix: 1.58 (0.29), residues: 372 sheet: -0.54 (0.15), residues: 1164 loop : -1.70 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 188 HIS 0.007 0.001 HIS G 125 PHE 0.027 0.001 PHE J 311 TYR 0.020 0.001 TYR B 357 ARG 0.007 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 862) hydrogen bonds : angle 4.93784 ( 2280) SS BOND : bond 0.00246 ( 84) SS BOND : angle 1.11557 ( 168) covalent geometry : bond 0.00351 (34712) covalent geometry : angle 0.58061 (47292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25144.44 seconds wall clock time: 440 minutes 42.24 seconds (26442.24 seconds total)