Starting phenix.real_space_refine on Fri May 30 11:56:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xi5_38371/05_2025/8xi5_38371_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xi5_38371/05_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_38371/05_2025/8xi5_38371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xi5_38371/05_2025/8xi5_38371.map" model { file = "/net/cci-nas-00/data/ceres_data/8xi5_38371/05_2025/8xi5_38371_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xi5_38371/05_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-5687/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: 19.35, per 1000 atoms: 0.57 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: 7.85 Conformation dependent library (CDL) restraints added in 4.2 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: 4.91 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: 12.00 Time building geometry restraints manager: 9.25 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.440 Check model and map are aligned: 0.270 Set scattering table: 0.340 Process input model: 72.120 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.190 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.240 ------------------------------------------------------------------------------- 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 : 3.956 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: 0.4375 time to fit residues: 260.2233 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 : 3.782 ------------------------------------------------------------------------------- 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 = 47315.348| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.16 r_work: 0.3058 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 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 1.14338 ( 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 : 3.731 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: 0.8957 (t80) cc_final: 0.8749 (t80) REVERT: B 384 TRP cc_start: 0.7127 (t60) cc_final: 0.6911 (t-100) REVERT: B 398 LYS cc_start: 0.8106 (tttm) cc_final: 0.7881 (tttm) REVERT: C 121 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.7069 (pm20) REVERT: C 217 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7949 (mm) REVERT: D 434 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6801 (mp) REVERT: E 41 HIS cc_start: 0.9063 (OUTLIER) cc_final: 0.7260 (t70) REVERT: E 199 CYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8248 (m) REVERT: E 292 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9152 (tt) REVERT: E 362 LEU cc_start: 0.8652 (mm) cc_final: 0.8356 (tp) REVERT: F 170 MET cc_start: 0.4238 (pmm) cc_final: 0.3939 (pmm) REVERT: G 368 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8686 (pt) REVERT: H 68 MET cc_start: 0.8391 (ptm) cc_final: 0.8160 (ptp) REVERT: J 45 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8094 (mt-10) REVERT: J 125 HIS cc_start: 0.6893 (OUTLIER) cc_final: 0.5591 (t-90) REVERT: J 192 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7858 (tp30) REVERT: J 328 ASN cc_start: 0.8724 (m110) cc_final: 0.8225 (t0) REVERT: J 370 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9075 (p) REVERT: J 438 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8591 (m-80) REVERT: L 186 TYR cc_start: 0.7561 (m-80) cc_final: 0.7234 (m-80) REVERT: L 195 TYR cc_start: 0.5173 (t80) cc_final: 0.4787 (t80) REVERT: S 111 ARG cc_start: 0.4089 (OUTLIER) cc_final: 0.3145 (tpt170) outliers start: 190 outliers final: 122 residues processed: 493 average time/residue: 0.4235 time to fit residues: 352.7590 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 : 3.757 ------------------------------------------------------------------------------- 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: 0.0870 chunk 79 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 291 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 369 optimal weight: 6.9990 chunk 312 optimal weight: 2.9990 chunk 320 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 397 optimal weight: 20.0000 overall best weight: 2.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 361 ASN D 369 GLN E 155 HIS E 168 GLN ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 GLN J 100 ASN K 94 HIS ** K 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3827 r_free = 0.3827 target = 0.161005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121351 restraints weight = 47637.591| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.23 r_work: 0.3062 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34796 Z= 0.127 Angle : 0.574 11.369 47460 Z= 0.300 Chirality : 0.044 0.204 5240 Planarity : 0.005 0.064 6128 Dihedral : 5.519 73.908 4724 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.94 % Allowed : 29.14 % Favored : 65.92 % 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: -1.91 (0.12), residues: 4336 helix: 0.05 (0.27), residues: 372 sheet: -0.60 (0.16), residues: 1160 loop : -1.85 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 188 HIS 0.005 0.001 HIS G 125 PHE 0.023 0.001 PHE G 311 TYR 0.019 0.001 TYR A 309 ARG 0.006 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 862) hydrogen bonds : angle 5.49652 ( 2280) SS BOND : bond 0.00278 ( 84) SS BOND : angle 0.97786 ( 168) covalent geometry : bond 0.00301 (34712) covalent geometry : angle 0.57184 (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 519 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 334 time to evaluate : 3.487 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: 0.8805 (mt) cc_final: 0.8539 (tp) REVERT: B 398 LYS cc_start: 0.8075 (tttm) cc_final: 0.7869 (tttm) REVERT: C 121 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.7050 (pm20) REVERT: C 217 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7881 (mm) REVERT: D 99 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7285 (tm-30) REVERT: D 282 ASP cc_start: 0.8916 (t70) cc_final: 0.8639 (t0) REVERT: D 316 ILE cc_start: 0.8444 (mt) cc_final: 0.8215 (tp) REVERT: D 410 TRP cc_start: 0.8377 (m100) cc_final: 0.7901 (m100) REVERT: E 41 HIS cc_start: 0.8966 (OUTLIER) cc_final: 0.6875 (t70) REVERT: E 199 CYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8311 (m) REVERT: E 292 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9094 (tt) REVERT: G 30 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: G 368 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8666 (pt) REVERT: H 284 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8931 (mt) REVERT: I 185 PHE cc_start: 0.4258 (OUTLIER) cc_final: 0.3630 (t80) REVERT: J 100 ASN cc_start: 0.7096 (OUTLIER) cc_final: 0.6852 (m-40) REVERT: J 125 HIS cc_start: 0.6693 (OUTLIER) cc_final: 0.5400 (t-90) REVERT: J 370 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8911 (p) REVERT: J 438 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: K 168 GLN cc_start: 0.8926 (tt0) cc_final: 0.8614 (tt0) REVERT: K 222 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7754 (pm20) REVERT: L 195 TYR cc_start: 0.4833 (t80) cc_final: 0.4439 (t80) REVERT: L 209 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7227 (tmtt) REVERT: L 214 ARG cc_start: 0.8695 (mmt90) cc_final: 0.8430 (mmt90) REVERT: S 111 ARG cc_start: 0.4058 (OUTLIER) cc_final: 0.3121 (tpt170) REVERT: S 137 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5799 (pm20) outliers start: 185 outliers final: 113 residues processed: 490 average time/residue: 0.4057 time to fit residues: 331.8624 Evaluate side-chains 443 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 313 time to evaluate : 3.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 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 322 LYS Chi-restraints excluded: chain A residue 354 THR 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 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain 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 C residue 240 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 292 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 206 VAL Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 411 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 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 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 I residue 249 VAL Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 100 ASN 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 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 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 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 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 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 314 VAL 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 237 THR Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain P residue 198 PHE Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 111 ARG Chi-restraints excluded: chain S residue 137 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 361 optimal weight: 5.9990 chunk 70 optimal weight: 0.0870 chunk 318 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 380 optimal weight: 4.9990 chunk 382 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN E 358 ASN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 439 HIS K 155 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.162662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123087 restraints weight = 47203.631| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.24 r_work: 0.3067 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34796 Z= 0.112 Angle : 0.555 11.143 47460 Z= 0.290 Chirality : 0.044 0.195 5240 Planarity : 0.004 0.054 6128 Dihedral : 5.318 71.849 4724 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 5.80 % Allowed : 28.21 % Favored : 66.00 % 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: -1.74 (0.12), residues: 4336 helix: 0.70 (0.28), residues: 372 sheet: -0.57 (0.15), residues: 1160 loop : -1.76 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 188 HIS 0.006 0.001 HIS K 155 PHE 0.020 0.001 PHE G 311 TYR 0.017 0.001 TYR A 309 ARG 0.007 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 862) hydrogen bonds : angle 5.20227 ( 2280) SS BOND : bond 0.00210 ( 84) SS BOND : angle 0.91606 ( 168) covalent geometry : bond 0.00264 (34712) covalent geometry : angle 0.55300 (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 552 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 335 time to evaluate : 3.568 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: 0.8828 (mt) cc_final: 0.8527 (tp) REVERT: B 200 LYS cc_start: 0.8187 (tppp) cc_final: 0.7952 (ttmt) REVERT: B 398 LYS cc_start: 0.8087 (tttm) cc_final: 0.7879 (tttm) REVERT: C 121 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.7026 (pm20) REVERT: C 217 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7887 (mm) REVERT: D 99 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7358 (tm-30) REVERT: D 316 ILE cc_start: 0.8472 (mt) cc_final: 0.8259 (tp) REVERT: D 410 TRP cc_start: 0.8417 (m100) cc_final: 0.7910 (m100) REVERT: D 436 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7562 (mp) REVERT: E 19 CYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8702 (t) REVERT: E 41 HIS cc_start: 0.8933 (OUTLIER) cc_final: 0.6856 (t70) REVERT: E 199 CYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8317 (m) REVERT: G 368 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8671 (pt) REVERT: H 50 SER cc_start: 0.9188 (OUTLIER) cc_final: 0.8971 (p) REVERT: H 74 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8390 (mtpp) REVERT: H 284 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8915 (mt) REVERT: H 300 ASP cc_start: 0.8001 (t0) cc_final: 0.7347 (p0) REVERT: I 185 PHE cc_start: 0.4246 (OUTLIER) cc_final: 0.3560 (t80) REVERT: J 370 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8928 (p) REVERT: J 438 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: K 168 GLN cc_start: 0.8948 (tt0) cc_final: 0.8660 (tt0) REVERT: K 222 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7786 (pm20) REVERT: L 195 TYR cc_start: 0.5387 (t80) cc_final: 0.4802 (t80) REVERT: L 209 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7216 (tmtt) REVERT: L 214 ARG cc_start: 0.8830 (mmt90) cc_final: 0.8492 (mmt90) REVERT: L 245 ASN cc_start: 0.8677 (p0) cc_final: 0.8282 (p0) REVERT: S 137 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5822 (pm20) outliers start: 217 outliers final: 153 residues processed: 520 average time/residue: 0.4136 time to fit residues: 361.3928 Evaluate side-chains 487 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 318 time to evaluate : 3.480 ------------------------------------------------------------------------------- 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 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 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 B residue 19 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 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 41 SER Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 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 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 321 GLU Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 399 LEU 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 6 VAL 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 183 HIS Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 411 ILE 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 41 HIS 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 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 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 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 153 THR 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 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 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 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 413 CYS Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 209 LYS Chi-restraints excluded: chain L residue 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 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: 9.9990 chunk 368 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 425 optimal weight: 50.0000 chunk 229 optimal weight: 0.9980 chunk 205 optimal weight: 9.9990 chunk 332 optimal weight: 9.9990 chunk 430 optimal weight: 0.0980 chunk 74 optimal weight: 0.6980 chunk 384 optimal weight: 7.9990 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 30 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS J 439 HIS K 41 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 = 0.3794 r_free = 0.3794 target = 0.157008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.117534 restraints weight = 47713.124| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.27 r_work: 0.3046 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34796 Z= 0.155 Angle : 0.583 10.132 47460 Z= 0.304 Chirality : 0.045 0.189 5240 Planarity : 0.004 0.056 6128 Dihedral : 5.332 70.526 4722 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 6.30 % Allowed : 27.54 % Favored : 66.16 % 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: -1.66 (0.12), residues: 4336 helix: 1.02 (0.28), residues: 372 sheet: -0.58 (0.15), residues: 1200 loop : -1.73 (0.11), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 188 HIS 0.006 0.001 HIS G 125 PHE 0.032 0.001 PHE J 311 TYR 0.020 0.001 TYR A 309 ARG 0.007 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 862) hydrogen bonds : angle 5.13682 ( 2280) SS BOND : bond 0.00333 ( 84) SS BOND : angle 1.05660 ( 168) covalent geometry : bond 0.00376 (34712) covalent geometry : angle 0.58051 (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 556 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 320 time to evaluate : 3.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.7031 (pm20) REVERT: C 217 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7898 (mm) REVERT: D 99 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7416 (tm-30) REVERT: D 410 TRP cc_start: 0.8431 (m100) cc_final: 0.7849 (m100) REVERT: D 436 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7687 (mp) REVERT: E 19 CYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8735 (t) REVERT: E 41 HIS cc_start: 0.8957 (OUTLIER) cc_final: 0.6941 (t70) REVERT: E 199 CYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8424 (m) REVERT: E 308 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8985 (mm) REVERT: E 388 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.6554 (mtp180) REVERT: G 368 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8561 (pt) REVERT: H 50 SER cc_start: 0.9185 (OUTLIER) cc_final: 0.8953 (p) REVERT: H 284 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8948 (mt) REVERT: H 300 ASP cc_start: 0.8109 (t0) cc_final: 0.7362 (p0) REVERT: I 169 CYS cc_start: 0.1903 (OUTLIER) cc_final: 0.1493 (t) REVERT: I 185 PHE cc_start: 0.4547 (OUTLIER) cc_final: 0.3644 (t80) REVERT: J 29 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9077 (tt) REVERT: J 103 MET cc_start: 0.8157 (mtp) cc_final: 0.7933 (ttm) REVERT: J 125 HIS cc_start: 0.6915 (OUTLIER) cc_final: 0.5341 (t-90) REVERT: J 328 ASN cc_start: 0.8636 (m110) cc_final: 0.8179 (t0) REVERT: J 370 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8991 (p) REVERT: J 421 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7257 (t80) REVERT: K 168 GLN cc_start: 0.9036 (tt0) cc_final: 0.8715 (tt0) REVERT: K 222 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: L 195 TYR cc_start: 0.5563 (t80) cc_final: 0.4987 (t80) REVERT: L 209 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7430 (tmtt) REVERT: L 245 ASN cc_start: 0.8614 (p0) cc_final: 0.8369 (p0) REVERT: S 111 ARG cc_start: 0.4401 (OUTLIER) cc_final: 0.3243 (tpt170) outliers start: 236 outliers final: 185 residues processed: 520 average time/residue: 0.4017 time to fit residues: 351.5325 Evaluate side-chains 513 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 308 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 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 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 151 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 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 41 SER Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 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 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 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 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 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 F residue 251 VAL Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 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 253 ASN Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 411 ILE Chi-restraints excluded: chain 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 133 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 346 HIS Chi-restraints excluded: chain H residue 371 CYS Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 393 CYS Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain I residue 138 HIS Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 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 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 126 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 253 ASN Chi-restraints excluded: chain J residue 282 ASP Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain 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 41 HIS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 222 GLN Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 346 HIS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 389 THR Chi-restraints excluded: chain K residue 413 CYS Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 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 Q residue 130 VAL Chi-restraints excluded: chain Q residue 134 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 111 ARG Chi-restraints excluded: chain T residue 130 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 141 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 329 optimal weight: 0.8980 chunk 175 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 331 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN D 226 GLN D 356 HIS G 30 GLN ** G 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 439 HIS K 41 HIS K 155 HIS K 194 GLN ** N 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116358 restraints weight = 47623.337| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.22 r_work: 0.3014 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 34796 Z= 0.209 Angle : 0.621 9.625 47460 Z= 0.324 Chirality : 0.047 0.192 5240 Planarity : 0.005 0.061 6128 Dihedral : 5.500 70.435 4722 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 7.13 % Allowed : 26.98 % Favored : 65.89 % 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: -1.70 (0.12), residues: 4336 helix: 1.07 (0.28), residues: 372 sheet: -0.65 (0.15), residues: 1248 loop : -1.76 (0.11), residues: 2716 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 0.040 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 0.04005 ( 862) hydrogen bonds : angle 5.18913 ( 2280) SS BOND : bond 0.00378 ( 84) SS BOND : angle 1.17275 ( 168) covalent geometry : bond 0.00512 (34712) covalent geometry : angle 0.61861 (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 572 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 305 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.7975 (tp) REVERT: B 168 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8355 (tt0) REVERT: C 121 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.7044 (pm20) REVERT: C 217 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7906 (mm) REVERT: D 67 GLN cc_start: 0.8830 (mp10) cc_final: 0.8582 (mp10) REVERT: D 99 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7330 (tm-30) REVERT: D 436 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7664 (mp) REVERT: E 19 CYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8756 (t) REVERT: E 41 HIS cc_start: 0.9061 (OUTLIER) cc_final: 0.7036 (t70) REVERT: E 199 CYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8123 (m) REVERT: E 308 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8997 (mm) REVERT: E 388 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.6230 (mtp180) REVERT: G 368 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8563 (pt) REVERT: H 50 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8928 (p) REVERT: H 284 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8893 (mt) REVERT: H 300 ASP cc_start: 0.8091 (t0) cc_final: 0.7314 (p0) REVERT: H 310 ARG cc_start: 0.8444 (mtm110) cc_final: 0.8237 (mtm110) REVERT: I 169 CYS cc_start: 0.2067 (OUTLIER) cc_final: 0.1859 (t) REVERT: I 185 PHE cc_start: 0.3681 (OUTLIER) cc_final: 0.2333 (t80) REVERT: J 29 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9105 (tp) REVERT: J 99 GLU cc_start: 0.8139 (pp20) cc_final: 0.7908 (pp20) REVERT: J 103 MET cc_start: 0.8311 (mtp) cc_final: 0.8054 (ttm) REVERT: J 125 HIS cc_start: 0.6934 (OUTLIER) cc_final: 0.5263 (t-90) REVERT: J 159 ASP cc_start: 0.8618 (t0) cc_final: 0.8264 (t0) REVERT: J 370 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.9006 (p) REVERT: J 421 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7131 (t80) REVERT: K 168 GLN cc_start: 0.9019 (tt0) cc_final: 0.8601 (tt0) REVERT: K 222 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7717 (pm20) REVERT: L 195 TYR cc_start: 0.5559 (t80) cc_final: 0.4954 (t80) REVERT: L 209 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7562 (tmtt) REVERT: L 245 ASN cc_start: 0.8554 (p0) cc_final: 0.8309 (p0) REVERT: P 220 ASP cc_start: 0.6563 (OUTLIER) cc_final: 0.6170 (p0) REVERT: S 111 ARG cc_start: 0.4416 (OUTLIER) cc_final: 0.3233 (tpt170) REVERT: S 137 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5838 (pm20) outliers start: 267 outliers final: 213 residues processed: 534 average time/residue: 0.4163 time to fit residues: 375.0738 Evaluate side-chains 538 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 301 time to evaluate : 3.706 ------------------------------------------------------------------------------- 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 130 GLN 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 322 LYS 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 151 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 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 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 228 LEU Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 235 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 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 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 22 CYS Chi-restraints excluded: chain H residue 24 HIS Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 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 209 THR Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 346 HIS Chi-restraints excluded: chain H residue 371 CYS Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 393 CYS Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 138 HIS Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 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 289 THR Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain J residue 439 HIS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 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 206 VAL Chi-restraints excluded: chain L residue 209 LYS Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 237 THR Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain P residue 206 ILE Chi-restraints excluded: chain P residue 209 SER Chi-restraints excluded: chain P residue 220 ASP Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 111 ARG Chi-restraints excluded: chain S residue 137 GLU 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: 1.9990 chunk 196 optimal weight: 20.0000 chunk 383 optimal weight: 8.9990 chunk 232 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 386 optimal weight: 0.8980 chunk 381 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 162 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN D 226 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 = 0.3807 r_free = 0.3807 target = 0.157966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118478 restraints weight = 47725.689| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.16 r_work: 0.3065 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34796 Z= 0.117 Angle : 0.563 9.752 47460 Z= 0.293 Chirality : 0.044 0.195 5240 Planarity : 0.004 0.058 6128 Dihedral : 5.276 69.558 4722 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 5.93 % Allowed : 28.31 % 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: -1.58 (0.12), residues: 4336 helix: 1.29 (0.29), residues: 372 sheet: -0.50 (0.15), residues: 1164 loop : -1.71 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 188 HIS 0.006 0.001 HIS G 125 PHE 0.022 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 0.03541 ( 862) hydrogen bonds : angle 4.99103 ( 2280) SS BOND : bond 0.00246 ( 84) SS BOND : angle 1.10818 ( 168) covalent geometry : bond 0.00279 (34712) covalent geometry : angle 0.55999 (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 538 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 316 time to evaluate : 3.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: C 121 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6972 (pm20) REVERT: C 217 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7976 (mm) REVERT: D 67 GLN cc_start: 0.8771 (mp10) cc_final: 0.8543 (mp10) REVERT: D 99 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7354 (tm-30) REVERT: D 436 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7691 (mp) REVERT: E 19 CYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8747 (t) REVERT: E 41 HIS cc_start: 0.8925 (OUTLIER) cc_final: 0.6841 (t70) REVERT: E 199 CYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8354 (m) REVERT: E 308 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8936 (mm) REVERT: E 388 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6277 (mtp180) REVERT: G 368 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8572 (pt) REVERT: H 50 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8927 (p) REVERT: H 284 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8894 (mt) REVERT: H 300 ASP cc_start: 0.8059 (t0) cc_final: 0.7338 (p0) REVERT: I 169 CYS cc_start: 0.1908 (OUTLIER) cc_final: 0.1698 (t) REVERT: I 185 PHE cc_start: 0.3707 (OUTLIER) cc_final: 0.2360 (t80) REVERT: J 29 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9076 (tt) REVERT: J 99 GLU cc_start: 0.8052 (pp20) cc_final: 0.7834 (pp20) REVERT: J 103 MET cc_start: 0.8252 (mtp) cc_final: 0.8033 (ttm) REVERT: J 125 HIS cc_start: 0.6835 (OUTLIER) cc_final: 0.5225 (t-90) REVERT: J 159 ASP cc_start: 0.8653 (t0) cc_final: 0.8433 (t0) REVERT: J 370 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8928 (p) REVERT: J 421 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7290 (t80) REVERT: K 168 GLN cc_start: 0.8996 (tt0) cc_final: 0.8603 (tt0) REVERT: K 222 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: L 195 TYR cc_start: 0.5564 (t80) cc_final: 0.4968 (t80) REVERT: L 209 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7443 (tmtt) REVERT: L 245 ASN cc_start: 0.8541 (p0) cc_final: 0.8267 (p0) REVERT: P 220 ASP cc_start: 0.6664 (OUTLIER) cc_final: 0.6266 (p0) REVERT: S 137 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5914 (pm20) outliers start: 222 outliers final: 178 residues processed: 506 average time/residue: 0.4283 time to fit residues: 363.8867 Evaluate side-chains 504 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 304 time to evaluate : 3.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 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 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 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 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 239 ARG 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 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 C residue 121 GLN 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 184 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 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 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 206 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 251 VAL 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 253 ASN 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 408 TRP Chi-restraints excluded: chain G residue 411 ILE Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain G residue 434 LEU 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 65 MET Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 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 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 169 CYS 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 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 282 ASP Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 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 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 314 VAL Chi-restraints excluded: chain K residue 346 HIS Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 389 THR Chi-restraints excluded: chain K residue 413 CYS Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 59 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 305 optimal weight: 9.9990 chunk 251 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 424 optimal weight: 3.9990 chunk 126 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 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 = 0.3799 r_free = 0.3799 target = 0.157280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.117648 restraints weight = 47279.013| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.14 r_work: 0.3063 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34796 Z= 0.147 Angle : 0.582 9.336 47460 Z= 0.302 Chirality : 0.045 0.203 5240 Planarity : 0.004 0.059 6128 Dihedral : 5.307 69.333 4722 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 6.22 % Allowed : 27.96 % Favored : 65.81 % 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: -1.58 (0.12), residues: 4336 helix: 1.37 (0.28), residues: 372 sheet: -0.53 (0.15), residues: 1172 loop : -1.71 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 188 HIS 0.006 0.001 HIS G 125 PHE 0.028 0.001 PHE J 311 TYR 0.020 0.001 TYR A 309 ARG 0.007 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 862) hydrogen bonds : angle 4.98408 ( 2280) SS BOND : bond 0.00272 ( 84) SS BOND : angle 1.16887 ( 168) covalent geometry : bond 0.00356 (34712) covalent geometry : angle 0.57882 (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 547 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 314 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.7991 (tp) REVERT: B 168 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: C 121 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6964 (pm20) REVERT: C 217 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7956 (mm) REVERT: D 67 GLN cc_start: 0.8770 (mp10) cc_final: 0.8551 (mp10) REVERT: D 99 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7368 (tm-30) REVERT: D 436 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7659 (mp) REVERT: E 19 CYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8750 (t) REVERT: E 41 HIS cc_start: 0.8943 (OUTLIER) cc_final: 0.6846 (t70) REVERT: E 199 CYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8503 (m) REVERT: E 308 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8955 (mm) REVERT: E 388 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6257 (mtp180) REVERT: G 368 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8584 (pt) REVERT: H 50 SER cc_start: 0.9157 (OUTLIER) cc_final: 0.8919 (p) REVERT: H 284 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8911 (mt) REVERT: H 300 ASP cc_start: 0.8076 (t0) cc_final: 0.7354 (p0) REVERT: H 310 ARG cc_start: 0.8585 (mtm110) cc_final: 0.8266 (mtm-85) REVERT: I 169 CYS cc_start: 0.1932 (OUTLIER) cc_final: 0.1716 (t) REVERT: I 185 PHE cc_start: 0.3784 (OUTLIER) cc_final: 0.2290 (t80) REVERT: J 29 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9079 (tt) REVERT: J 99 GLU cc_start: 0.8042 (pp20) cc_final: 0.7836 (pp20) REVERT: J 103 MET cc_start: 0.8176 (mtp) cc_final: 0.7962 (ttm) REVERT: J 125 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.5229 (t-90) REVERT: J 421 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7344 (t80) REVERT: K 168 GLN cc_start: 0.9002 (tt0) cc_final: 0.8597 (tt0) REVERT: K 222 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7689 (pm20) REVERT: L 195 TYR cc_start: 0.5643 (t80) cc_final: 0.5041 (t80) REVERT: L 209 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7516 (tmtt) REVERT: L 245 ASN cc_start: 0.8527 (p0) cc_final: 0.8280 (p0) REVERT: P 220 ASP cc_start: 0.6710 (OUTLIER) cc_final: 0.6305 (p0) REVERT: S 137 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5935 (pm20) outliers start: 233 outliers final: 194 residues processed: 514 average time/residue: 0.4406 time to fit residues: 381.8021 Evaluate side-chains 527 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 311 time to evaluate : 3.812 ------------------------------------------------------------------------------- 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 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 157 ILE Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain 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 164 VAL Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 239 ARG 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 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 C residue 121 GLN 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 133 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 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 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 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 117 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 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 253 ASN 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 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 22 CYS Chi-restraints excluded: chain H residue 24 HIS Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 65 MET Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 305 ARG Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 346 HIS Chi-restraints excluded: chain H residue 371 CYS Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 393 CYS Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain I residue 138 HIS Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 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 29 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 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 368 LEU Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain K residue 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 206 VAL Chi-restraints excluded: chain L residue 209 LYS Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 227 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 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: 10.0000 chunk 138 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 314 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 289 optimal weight: 10.0000 chunk 293 optimal weight: 30.0000 chunk 375 optimal weight: 0.9980 chunk 269 optimal weight: 0.5980 overall best weight: 4.3184 ------------------------------------------------------------------------------- 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 332 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.116686 restraints weight = 47632.515| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.27 r_work: 0.3024 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 34796 Z= 0.186 Angle : 0.610 9.609 47460 Z= 0.317 Chirality : 0.046 0.200 5240 Planarity : 0.004 0.061 6128 Dihedral : 5.428 70.006 4722 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 6.38 % Allowed : 27.88 % 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: -1.60 (0.12), residues: 4336 helix: 1.37 (0.28), residues: 372 sheet: -0.55 (0.15), residues: 1172 loop : -1.73 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 210 HIS 0.006 0.001 HIS G 125 PHE 0.036 0.002 PHE J 311 TYR 0.022 0.002 TYR A 309 ARG 0.007 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 862) hydrogen bonds : angle 5.05132 ( 2280) SS BOND : bond 0.00322 ( 84) SS BOND : angle 1.22844 ( 168) covalent geometry : bond 0.00455 (34712) covalent geometry : angle 0.60684 (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 544 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 305 time to evaluate : 3.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7883 (m-10) REVERT: B 31 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8009 (tp) REVERT: B 168 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: C 121 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6988 (pm20) REVERT: C 217 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8021 (mm) REVERT: D 67 GLN cc_start: 0.8805 (mp10) cc_final: 0.8575 (mp10) REVERT: D 99 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7343 (tm-30) REVERT: D 436 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7627 (mp) REVERT: E 19 CYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8760 (t) REVERT: E 41 HIS cc_start: 0.9008 (OUTLIER) cc_final: 0.6915 (t70) REVERT: E 199 CYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8431 (m) REVERT: E 308 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8984 (mm) REVERT: E 388 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.6227 (mtp180) REVERT: G 368 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8524 (pt) REVERT: H 50 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8914 (p) REVERT: H 284 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8899 (mt) REVERT: H 300 ASP cc_start: 0.8122 (t0) cc_final: 0.7367 (p0) REVERT: I 185 PHE cc_start: 0.3875 (OUTLIER) cc_final: 0.2335 (t80) REVERT: J 29 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9104 (tt) REVERT: J 99 GLU cc_start: 0.8172 (pp20) cc_final: 0.7951 (pp20) REVERT: J 103 MET cc_start: 0.8247 (mtp) cc_final: 0.8044 (ttm) REVERT: J 125 HIS cc_start: 0.6892 (OUTLIER) cc_final: 0.5243 (t-90) REVERT: J 421 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7311 (t80) REVERT: K 168 GLN cc_start: 0.9058 (tt0) cc_final: 0.8653 (tt0) REVERT: K 222 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: L 209 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7569 (tmtt) REVERT: L 245 ASN cc_start: 0.8516 (p0) cc_final: 0.8285 (p0) REVERT: P 220 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.6322 (p0) REVERT: S 137 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5864 (pm20) outliers start: 239 outliers final: 203 residues processed: 508 average time/residue: 0.3931 time to fit residues: 336.9984 Evaluate side-chains 526 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 301 time to evaluate : 3.710 ------------------------------------------------------------------------------- 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 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 164 VAL Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 121 GLN 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 116 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 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 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 166 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 253 ASN 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 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 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 61 ASP Chi-restraints excluded: chain H residue 65 MET Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 305 ARG Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 346 HIS Chi-restraints excluded: chain H residue 371 CYS Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 393 CYS Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain 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 29 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 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 368 LEU Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 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 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 227 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 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: 8.9990 chunk 187 optimal weight: 5.9990 chunk 416 optimal weight: 8.9990 chunk 369 optimal weight: 5.9990 chunk 396 optimal weight: 0.8980 chunk 203 optimal weight: 9.9990 chunk 399 optimal weight: 10.0000 chunk 360 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 387 optimal weight: 0.1980 overall best weight: 4.0186 ------------------------------------------------------------------------------- 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** I 168 GLN 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 = 0.3801 r_free = 0.3801 target = 0.158673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.118700 restraints weight = 47112.578| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.16 r_work: 0.3033 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34796 Z= 0.177 Angle : 0.611 11.425 47460 Z= 0.318 Chirality : 0.046 0.224 5240 Planarity : 0.005 0.063 6128 Dihedral : 5.450 70.317 4722 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 6.17 % Allowed : 27.99 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.60 (0.12), residues: 4336 helix: 1.41 (0.28), residues: 372 sheet: -0.57 (0.15), residues: 1172 loop : -1.72 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 210 HIS 0.006 0.001 HIS G 125 PHE 0.034 0.002 PHE J 311 TYR 0.022 0.001 TYR B 357 ARG 0.007 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 862) hydrogen bonds : angle 5.05543 ( 2280) SS BOND : bond 0.00307 ( 84) SS BOND : angle 1.16254 ( 168) covalent geometry : bond 0.00432 (34712) covalent geometry : angle 0.60799 (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 533 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 302 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.7986 (tp) REVERT: B 168 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: B 222 GLN cc_start: 0.8273 (pm20) cc_final: 0.7828 (pm20) REVERT: C 121 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6999 (pm20) REVERT: C 217 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8076 (mm) REVERT: D 67 GLN cc_start: 0.8804 (mp10) cc_final: 0.8566 (mp10) REVERT: D 99 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7309 (tm-30) REVERT: D 436 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7607 (mp) REVERT: E 19 CYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8741 (t) REVERT: E 41 HIS cc_start: 0.9011 (OUTLIER) cc_final: 0.6899 (t70) REVERT: E 199 CYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8362 (m) REVERT: E 308 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8972 (mm) REVERT: E 388 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6292 (mtp180) REVERT: G 368 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8504 (pt) REVERT: H 50 SER cc_start: 0.9136 (OUTLIER) cc_final: 0.8893 (p) REVERT: H 284 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8884 (mt) REVERT: H 300 ASP cc_start: 0.8096 (t0) cc_final: 0.7343 (p0) REVERT: I 185 PHE cc_start: 0.4158 (OUTLIER) cc_final: 0.2658 (t80) REVERT: J 29 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9098 (tt) REVERT: J 103 MET cc_start: 0.8168 (mtp) cc_final: 0.7941 (ttm) REVERT: J 125 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.5206 (t-90) REVERT: J 421 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7505 (t80) REVERT: K 168 GLN cc_start: 0.9057 (tt0) cc_final: 0.8629 (tt0) REVERT: K 222 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7679 (pm20) REVERT: L 188 TRP cc_start: 0.7293 (OUTLIER) cc_final: 0.4859 (t-100) REVERT: L 209 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7585 (tmtt) REVERT: L 245 ASN cc_start: 0.8509 (p0) cc_final: 0.8278 (p0) REVERT: P 220 ASP cc_start: 0.6704 (OUTLIER) cc_final: 0.6319 (p0) REVERT: S 111 ARG cc_start: 0.4421 (OUTLIER) cc_final: 0.3349 (tpt170) REVERT: S 137 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5926 (pm20) outliers start: 231 outliers final: 204 residues processed: 502 average time/residue: 0.4033 time to fit residues: 341.6483 Evaluate side-chains 525 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 298 time to evaluate : 3.749 ------------------------------------------------------------------------------- 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 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 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 164 VAL Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 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 296 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 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 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 166 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 253 ASN 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 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 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 61 ASP Chi-restraints excluded: chain H residue 65 MET Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 305 ARG Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 346 HIS Chi-restraints excluded: chain H residue 371 CYS Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 393 CYS Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain 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 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 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 368 LEU Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 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 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 227 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: 7.9990 chunk 246 optimal weight: 7.9990 chunk 414 optimal weight: 30.0000 chunk 128 optimal weight: 5.9990 chunk 399 optimal weight: 20.0000 chunk 270 optimal weight: 0.6980 chunk 390 optimal weight: 1.9990 chunk 372 optimal weight: 2.9990 chunk 344 optimal weight: 2.9990 chunk 358 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.159677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119597 restraints weight = 47105.157| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.14 r_work: 0.3011 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34796 Z= 0.143 Angle : 0.590 11.831 47460 Z= 0.307 Chirality : 0.045 0.216 5240 Planarity : 0.004 0.062 6128 Dihedral : 5.366 69.997 4722 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 6.28 % Allowed : 27.83 % Favored : 65.89 % 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: -1.56 (0.13), residues: 4336 helix: 1.51 (0.28), residues: 372 sheet: -0.55 (0.15), residues: 1172 loop : -1.70 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 188 HIS 0.006 0.001 HIS G 125 PHE 0.032 0.001 PHE A 95 TYR 0.020 0.001 TYR B 357 ARG 0.007 0.000 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 862) hydrogen bonds : angle 4.99197 ( 2280) SS BOND : bond 0.00265 ( 84) SS BOND : angle 1.10593 ( 168) covalent geometry : bond 0.00346 (34712) covalent geometry : angle 0.58733 (47292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19823.49 seconds wall clock time: 343 minutes 45.33 seconds (20625.33 seconds total)