Starting phenix.real_space_refine on Sat Jun 28 18:15:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xi4_38370/06_2025/8xi4_38370.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xi4_38370/06_2025/8xi4_38370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xi4_38370/06_2025/8xi4_38370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xi4_38370/06_2025/8xi4_38370.map" model { file = "/net/cci-nas-00/data/ceres_data/8xi4_38370/06_2025/8xi4_38370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xi4_38370/06_2025/8xi4_38370.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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 244 5.16 5 C 21320 2.51 5 N 5876 2.21 5 O 6324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 224 residue(s): 0.41s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33772 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3375 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 411} Chain: "B" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3300 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 32, 'TRANS': 387} Chain: "C" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1165 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "D" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3375 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 411} Chain: "E" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3300 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 32, 'TRANS': 387} Chain: "F" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1165 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "G" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3375 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 411} Chain: "H" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3300 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 32, 'TRANS': 387} Chain: "I" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1165 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "J" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3375 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 411} Chain: "K" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3300 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 32, 'TRANS': 387} Chain: "L" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1165 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "M" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 601 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "N" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 601 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "O" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 601 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "P" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 601 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.96, per 1000 atoms: 0.56 Number of scatterers: 33772 At special positions: 0 Unit cell: (175.5, 201.15, 214.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 244 16.00 O 6324 8.00 N 5876 7.00 C 21320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=84, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 272 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=2.03 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 103 " distance=1.87 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 217 " distance=2.50 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 414 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 260 " - pdb=" SG CYS D 272 " distance=1.89 Simple disulfide: pdb=" SG CYS D 302 " - pdb=" SG CYS D 377 " distance=2.03 Simple disulfide: pdb=" SG CYS D 307 " - pdb=" SG CYS D 381 " distance=2.03 Simple disulfide: pdb=" SG CYS D 329 " - pdb=" SG CYS D 371 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 27 " distance=2.03 Simple disulfide: pdb=" SG CYS E 89 " - pdb=" SG CYS E 103 " distance=2.03 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 199 " - pdb=" SG CYS E 223 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 217 " distance=2.50 Simple disulfide: pdb=" SG CYS E 393 " - pdb=" SG CYS E 414 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=1.72 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 260 " - pdb=" SG CYS G 272 " distance=2.03 Simple disulfide: pdb=" SG CYS G 302 " - pdb=" SG CYS G 377 " distance=2.03 Simple disulfide: pdb=" SG CYS G 307 " - pdb=" SG CYS G 381 " distance=2.03 Simple disulfide: pdb=" SG CYS G 329 " - pdb=" SG CYS G 371 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 27 " distance=2.03 Simple disulfide: pdb=" SG CYS H 89 " - pdb=" SG CYS H 103 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 263 " distance=2.03 Simple disulfide: pdb=" SG CYS H 199 " - pdb=" SG CYS H 223 " distance=2.03 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 217 " distance=2.50 Simple disulfide: pdb=" SG CYS H 393 " - pdb=" SG CYS H 414 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 260 " - pdb=" SG CYS J 272 " distance=2.03 Simple disulfide: pdb=" SG CYS J 302 " - pdb=" SG CYS J 377 " distance=2.03 Simple disulfide: pdb=" SG CYS J 307 " - pdb=" SG CYS J 381 " distance=2.16 Simple disulfide: pdb=" SG CYS J 329 " - pdb=" SG CYS J 371 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 122 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 27 " distance=2.03 Simple disulfide: pdb=" SG CYS K 89 " - pdb=" SG CYS K 103 " distance=2.03 Simple disulfide: pdb=" SG CYS K 150 " - pdb=" SG CYS K 263 " distance=1.72 Simple disulfide: pdb=" SG CYS K 199 " - pdb=" SG CYS K 223 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 217 " distance=2.50 Simple disulfide: pdb=" SG CYS K 393 " - pdb=" SG CYS K 414 " distance=2.03 Simple disulfide: pdb=" SG CYS M 33 " - pdb=" SG CYS M 45 " distance=2.03 Simple disulfide: pdb=" SG CYS M 40 " - pdb=" SG CYS M 58 " distance=2.04 Simple disulfide: pdb=" SG CYS M 52 " - pdb=" SG CYS M 67 " distance=2.03 Simple disulfide: pdb=" SG CYS M 72 " - pdb=" SG CYS M 84 " distance=2.03 Simple disulfide: pdb=" SG CYS M 79 " - pdb=" SG CYS M 97 " distance=2.03 Simple disulfide: pdb=" SG CYS M 91 " - pdb=" SG CYS M 108 " distance=2.03 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 45 " distance=2.03 Simple disulfide: pdb=" SG CYS N 40 " - pdb=" SG CYS N 58 " distance=2.04 Simple disulfide: pdb=" SG CYS N 52 " - pdb=" SG CYS N 67 " distance=2.03 Simple disulfide: pdb=" SG CYS N 72 " - pdb=" SG CYS N 84 " distance=2.03 Simple disulfide: pdb=" SG CYS N 79 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 108 " distance=2.03 Simple disulfide: pdb=" SG CYS O 33 " - pdb=" SG CYS O 45 " distance=2.03 Simple disulfide: pdb=" SG CYS O 40 " - pdb=" SG CYS O 58 " distance=2.04 Simple disulfide: pdb=" SG CYS O 52 " - pdb=" SG CYS O 67 " distance=2.03 Simple disulfide: pdb=" SG CYS O 72 " - pdb=" SG CYS O 84 " distance=2.03 Simple disulfide: pdb=" SG CYS O 79 " - pdb=" SG CYS O 97 " distance=2.03 Simple disulfide: pdb=" SG CYS O 91 " - pdb=" SG CYS O 108 " distance=2.03 Simple disulfide: pdb=" SG CYS P 33 " - pdb=" SG CYS P 45 " distance=2.03 Simple disulfide: pdb=" SG CYS P 40 " - pdb=" SG CYS P 58 " distance=2.04 Simple disulfide: pdb=" SG CYS P 52 " - pdb=" SG CYS P 67 " distance=2.03 Simple disulfide: pdb=" SG CYS P 72 " - pdb=" SG CYS P 84 " distance=2.03 Simple disulfide: pdb=" SG CYS P 79 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS P 91 " - pdb=" SG CYS P 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.33 Conformation dependent library (CDL) restraints added in 4.3 seconds 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 92 sheets defined 12.6% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.79 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.990A pdb=" N SER A 115 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.545A pdb=" N VAL A 255 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.226A pdb=" N GLY A 259 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS A 260 " --> pdb=" O PRO A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.646A pdb=" N PHE A 288 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.641A pdb=" N THR A 294 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 441 removed outlier: 4.862A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 360 removed outlier: 3.763A pdb=" N VAL B 353 " --> pdb=" O PRO B 349 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL B 354 " --> pdb=" O HIS B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 395 removed outlier: 3.729A pdb=" N CYS B 369 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 4.368A pdb=" N LEU B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.834A pdb=" N MET C 170 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 171 " --> pdb=" O GLN C 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 167 through 171' Processing helix chain 'D' and resid 239 through 248 removed outlier: 3.591A pdb=" N LYS D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.837A pdb=" N PHE D 288 " --> pdb=" O ASP D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.882A pdb=" N THR D 294 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 441 removed outlier: 3.523A pdb=" N TRP D 410 " --> pdb=" O THR D 406 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 415 " --> pdb=" O ILE D 411 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 430 " --> pdb=" O LEU D 426 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 432 " --> pdb=" O ALA D 428 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 433 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS D 441 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 360 removed outlier: 3.801A pdb=" N VAL E 353 " --> pdb=" O PRO E 349 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL E 354 " --> pdb=" O HIS E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 399 removed outlier: 3.746A pdb=" N ILE E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 366 " --> pdb=" O LEU E 362 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR E 370 " --> pdb=" O ILE E 366 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE E 394 " --> pdb=" O ARG E 390 " (cutoff:3.500A) Proline residue: E 396 - end of helix removed outlier: 3.997A pdb=" N LEU E 399 " --> pdb=" O THR E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 removed outlier: 3.958A pdb=" N LEU E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU E 412 " --> pdb=" O LEU E 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 407 through 412' Processing helix chain 'F' and resid 145 through 150 removed outlier: 3.951A pdb=" N ALA F 150 " --> pdb=" O GLU F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 171 removed outlier: 4.030A pdb=" N MET F 170 " --> pdb=" O PRO F 167 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS F 171 " --> pdb=" O GLN F 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 167 through 171' Processing helix chain 'G' and resid 112 through 116 removed outlier: 4.202A pdb=" N SER G 115 " --> pdb=" O GLU G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 247 Processing helix chain 'G' and resid 251 through 255 Processing helix chain 'G' and resid 284 through 288 removed outlier: 3.588A pdb=" N ALA G 287 " --> pdb=" O PRO G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 411 Processing helix chain 'G' and resid 416 through 441 removed outlier: 3.619A pdb=" N VAL G 423 " --> pdb=" O SER G 419 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA G 428 " --> pdb=" O LEU G 424 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR G 429 " --> pdb=" O GLY G 425 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU G 434 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG G 440 " --> pdb=" O LEU G 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 360 removed outlier: 3.615A pdb=" N VAL H 353 " --> pdb=" O PRO H 349 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL H 354 " --> pdb=" O HIS H 350 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN H 358 " --> pdb=" O VAL H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 380 Processing helix chain 'H' and resid 385 through 399 removed outlier: 3.900A pdb=" N ILE H 394 " --> pdb=" O ARG H 390 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR H 395 " --> pdb=" O ASN H 391 " (cutoff:3.500A) Proline residue: H 396 - end of helix removed outlier: 3.876A pdb=" N LEU H 399 " --> pdb=" O THR H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 411 removed outlier: 3.679A pdb=" N LEU H 411 " --> pdb=" O ILE H 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 171 removed outlier: 3.668A pdb=" N MET I 170 " --> pdb=" O PRO I 167 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS I 171 " --> pdb=" O GLN I 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 167 through 171' Processing helix chain 'J' and resid 112 through 116 removed outlier: 4.042A pdb=" N SER J 115 " --> pdb=" O GLU J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 248 removed outlier: 3.804A pdb=" N LYS J 246 " --> pdb=" O GLU J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 256 Processing helix chain 'J' and resid 257 through 260 Processing helix chain 'J' and resid 284 through 288 removed outlier: 3.726A pdb=" N PHE J 288 " --> pdb=" O ASP J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 294 Processing helix chain 'J' and resid 404 through 441 removed outlier: 3.500A pdb=" N GLY J 425 " --> pdb=" O PHE J 421 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL J 432 " --> pdb=" O ALA J 428 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA J 433 " --> pdb=" O THR J 429 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU J 434 " --> pdb=" O ALA J 430 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL J 435 " --> pdb=" O VAL J 431 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG J 440 " --> pdb=" O LEU J 436 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS J 441 " --> pdb=" O PHE J 437 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 6 Processing helix chain 'K' and resid 348 through 360 removed outlier: 3.520A pdb=" N VAL K 353 " --> pdb=" O PRO K 349 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL K 354 " --> pdb=" O HIS K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 392 removed outlier: 3.573A pdb=" N CYS K 369 " --> pdb=" O ILE K 365 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS K 371 " --> pdb=" O GLY K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 394 through 399 removed outlier: 3.541A pdb=" N LEU K 399 " --> pdb=" O THR K 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 151 removed outlier: 3.696A pdb=" N ALA L 150 " --> pdb=" O GLN L 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 51 No H-bonds generated for 'chain 'M' and resid 49 through 51' Processing helix chain 'M' and resid 61 through 65 removed outlier: 3.589A pdb=" N GLU M 64 " --> pdb=" O GLY M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 90 No H-bonds generated for 'chain 'M' and resid 88 through 90' Processing helix chain 'N' and resid 49 through 51 No H-bonds generated for 'chain 'N' and resid 49 through 51' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'O' and resid 49 through 51 No H-bonds generated for 'chain 'O' and resid 49 through 51' Processing helix chain 'O' and resid 61 through 65 Processing helix chain 'O' and resid 88 through 90 No H-bonds generated for 'chain 'O' and resid 88 through 90' Processing helix chain 'O' and resid 100 through 104 removed outlier: 3.686A pdb=" N GLU O 103 " --> pdb=" O GLY O 100 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER O 104 " --> pdb=" O SER O 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 100 through 104' Processing helix chain 'P' and resid 49 through 51 No H-bonds generated for 'chain 'P' and resid 49 through 51' Processing helix chain 'P' and resid 61 through 65 removed outlier: 3.787A pdb=" N LYS P 65 " --> pdb=" O SER P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 90 No H-bonds generated for 'chain 'P' and resid 88 through 90' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 3.614A pdb=" N VAL A 27 " --> pdb=" O VAL A 19 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 27 through 33 current: chain 'A' and resid 119 through 137 removed outlier: 3.720A pdb=" N VAL A 133 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 145 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR A 137 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N SER A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 140 through 148 current: chain 'A' and resid 184 through 187 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 184 through 187 current: chain 'A' and resid 215 through 216 Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.641A pdb=" N TYR A 107 " --> pdb=" O LYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 61 removed outlier: 3.773A pdb=" N THR A 101 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA6, first strand: chain 'A' and resid 297 through 307 removed outlier: 4.941A pdb=" N ASP A 299 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS A 322 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 316 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.702A pdb=" N VAL A 345 " --> pdb=" O CYS A 329 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS A 329 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA9, first strand: chain 'B' and resid 17 through 19 removed outlier: 3.626A pdb=" N ALA B 17 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 34 through 37 removed outlier: 4.776A pdb=" N VAL B 36 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG B 46 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 10.244A pdb=" N SER B 50 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N MET B 68 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR B 64 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.502A pdb=" N ASP B 107 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 153 Processing sheet with id=AB4, first strand: chain 'B' and resid 163 through 164 Processing sheet with id=AB5, first strand: chain 'B' and resid 166 through 167 Processing sheet with id=AB6, first strand: chain 'B' and resid 178 through 180 Processing sheet with id=AB7, first strand: chain 'B' and resid 204 through 208 removed outlier: 3.639A pdb=" N GLY B 207 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 272 through 275 Processing sheet with id=AB9, first strand: chain 'C' and resid 113 through 118 removed outlier: 4.554A pdb=" N GLY C 124 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU C 118 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 187 through 188 Processing sheet with id=AC2, first strand: chain 'C' and resid 215 through 217 removed outlier: 6.741A pdb=" N ILE C 216 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N VAL C 224 " --> pdb=" O TRP C 244 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TRP C 244 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE C 226 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER C 240 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AC4, first strand: chain 'D' and resid 15 through 19 removed outlier: 3.656A pdb=" N VAL D 27 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N MET D 132 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR D 36 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLN D 130 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 145 " --> pdb=" O VAL D 133 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 143 through 148 current: chain 'D' and resid 269 through 270 Processing sheet with id=AC5, first strand: chain 'D' and resid 41 through 48 removed outlier: 3.548A pdb=" N ASN D 43 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA D 121 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.696A pdb=" N TYR D 107 " --> pdb=" O LYS D 54 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AC8, first strand: chain 'D' and resid 204 through 206 Processing sheet with id=AC9, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AD1, first strand: chain 'D' and resid 297 through 306 removed outlier: 6.909A pdb=" N LEU D 300 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LYS D 322 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N CYS D 302 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA D 320 " --> pdb=" O CYS D 302 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE D 304 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR D 318 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU D 306 " --> pdb=" O ILE D 316 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 344 through 347 removed outlier: 3.905A pdb=" N VAL D 345 " --> pdb=" O CYS D 329 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS D 329 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS D 332 " --> pdb=" O GLN D 369 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AD4, first strand: chain 'E' and resid 17 through 18 removed outlier: 3.714A pdb=" N ALA E 17 " --> pdb=" O SER E 29 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 34 through 37 removed outlier: 3.524A pdb=" N GLN E 48 " --> pdb=" O GLU E 34 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL E 36 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG E 46 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 10.058A pdb=" N SER E 50 " --> pdb=" O MET E 68 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N MET E 68 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR E 64 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN E 69 " --> pdb=" O THR E 72 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 81 through 84 removed outlier: 4.572A pdb=" N ASP E 107 " --> pdb=" O HIS E 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 146 through 153 Processing sheet with id=AD8, first strand: chain 'E' and resid 234 through 235 Processing sheet with id=AD9, first strand: chain 'E' and resid 178 through 180 Processing sheet with id=AE1, first strand: chain 'E' and resid 204 through 208 removed outlier: 3.639A pdb=" N GLY E 207 " --> pdb=" O TYR E 197 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 272 through 276 removed outlier: 3.967A pdb=" N THR E 279 " --> pdb=" O LYS E 276 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 121 through 127 removed outlier: 5.213A pdb=" N VAL F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU F 118 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY F 124 " --> pdb=" O ILE F 116 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 186 through 187 Processing sheet with id=AE5, first strand: chain 'F' and resid 215 through 217 removed outlier: 6.562A pdb=" N ILE F 216 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N VAL F 224 " --> pdb=" O TRP F 244 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP F 244 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE F 226 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER F 240 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 2 through 8 removed outlier: 3.602A pdb=" N ALA G 5 " --> pdb=" O ILE G 279 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS G 161 " --> pdb=" O ASP G 282 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE G 157 " --> pdb=" O ALA G 160 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 14 through 21 removed outlier: 3.625A pdb=" N VAL G 27 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG G 21 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ALA G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU G 29 " --> pdb=" O TYR G 137 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR G 137 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE G 31 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE G 135 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU G 33 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL G 133 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN G 35 " --> pdb=" O ALA G 131 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA G 131 " --> pdb=" O ASN G 35 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ARG G 37 " --> pdb=" O VAL G 129 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL G 129 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE G 39 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY G 127 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA G 121 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE G 47 " --> pdb=" O ALA G 119 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA G 119 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL G 133 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA G 145 " --> pdb=" O VAL G 133 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 143 through 148 current: chain 'G' and resid 184 through 187 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 184 through 187 current: chain 'G' and resid 215 through 216 Processing sheet with id=AE8, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.636A pdb=" N TYR G 107 " --> pdb=" O LYS G 54 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 60 through 61 removed outlier: 3.637A pdb=" N PHE G 81 " --> pdb=" O GLN G 102 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AF2, first strand: chain 'G' and resid 261 through 262 Processing sheet with id=AF3, first strand: chain 'G' and resid 297 through 306 removed outlier: 6.986A pdb=" N LEU G 300 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LYS G 322 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N CYS G 302 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ALA G 320 " --> pdb=" O CYS G 302 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE G 304 " --> pdb=" O THR G 318 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR G 318 " --> pdb=" O ILE G 304 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE G 353 " --> pdb=" O VAL G 319 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 331 through 332 Processing sheet with id=AF5, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AF6, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=AF7, first strand: chain 'H' and resid 34 through 37 removed outlier: 3.535A pdb=" N GLN H 48 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL H 36 " --> pdb=" O ARG H 46 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG H 46 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 68 through 69 Processing sheet with id=AF9, first strand: chain 'H' and resid 81 through 84 removed outlier: 4.422A pdb=" N ASP H 107 " --> pdb=" O HIS H 126 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 146 through 153 Processing sheet with id=AG2, first strand: chain 'H' and resid 234 through 235 removed outlier: 3.664A pdb=" N GLY H 250 " --> pdb=" O MET H 166 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 178 through 180 Processing sheet with id=AG4, first strand: chain 'H' and resid 204 through 208 removed outlier: 3.638A pdb=" N GLY H 207 " --> pdb=" O TYR H 197 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 272 through 276 removed outlier: 3.758A pdb=" N THR H 279 " --> pdb=" O LYS H 276 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 114 through 118 removed outlier: 4.629A pdb=" N GLY I 124 " --> pdb=" O ILE I 116 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU I 118 " --> pdb=" O VAL I 122 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL I 122 " --> pdb=" O LEU I 118 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 128 through 129 removed outlier: 3.885A pdb=" N VAL I 129 " --> pdb=" O ARG I 132 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 186 through 188 Processing sheet with id=AG9, first strand: chain 'I' and resid 215 through 217 removed outlier: 9.866A pdb=" N VAL I 224 " --> pdb=" O TRP I 244 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N TRP I 244 " --> pdb=" O VAL I 224 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE I 226 " --> pdb=" O VAL I 242 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 2 through 8 Processing sheet with id=AH2, first strand: chain 'J' and resid 15 through 19 removed outlier: 6.396A pdb=" N MET J 132 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR J 36 " --> pdb=" O GLN J 130 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN J 130 " --> pdb=" O THR J 36 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TYR J 137 " --> pdb=" O SER J 141 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER J 141 " --> pdb=" O TYR J 137 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 184 through 186 removed outlier: 6.680A pdb=" N ALA J 119 " --> pdb=" O ILE J 47 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE J 47 " --> pdb=" O ALA J 119 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA J 121 " --> pdb=" O GLU J 45 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 51 through 54 Processing sheet with id=AH5, first strand: chain 'J' and resid 60 through 61 Processing sheet with id=AH6, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AH7, first strand: chain 'J' and resid 297 through 306 removed outlier: 5.733A pdb=" N ASP J 299 " --> pdb=" O LYS J 322 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS J 322 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE J 316 " --> pdb=" O THR J 305 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 344 through 347 removed outlier: 3.522A pdb=" N VAL J 345 " --> pdb=" O CYS J 329 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY J 327 " --> pdb=" O LEU J 347 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 388 through 389 Processing sheet with id=AI1, first strand: chain 'K' and resid 17 through 18 removed outlier: 3.547A pdb=" N ALA K 17 " --> pdb=" O SER K 29 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 34 through 37 removed outlier: 3.635A pdb=" N GLN K 48 " --> pdb=" O GLU K 34 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL K 36 " --> pdb=" O ARG K 46 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG K 46 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N SER K 50 " --> pdb=" O MET K 68 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET K 68 " --> pdb=" O SER K 50 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 81 through 84 removed outlier: 4.461A pdb=" N ASP K 107 " --> pdb=" O HIS K 126 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 146 through 153 removed outlier: 3.619A pdb=" N CYS K 150 " --> pdb=" O ALA K 261 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 163 through 164 Processing sheet with id=AI6, first strand: chain 'K' and resid 166 through 167 Processing sheet with id=AI7, first strand: chain 'K' and resid 178 through 180 Processing sheet with id=AI8, first strand: chain 'K' and resid 207 through 208 removed outlier: 3.638A pdb=" N GLY K 207 " --> pdb=" O TYR K 197 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'K' and resid 272 through 276 Processing sheet with id=AJ1, first strand: chain 'L' and resid 133 through 134 removed outlier: 5.298A pdb=" N VAL L 122 " --> pdb=" O LEU L 118 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU L 118 " --> pdb=" O VAL L 122 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY L 124 " --> pdb=" O ILE L 116 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 186 through 188 Processing sheet with id=AJ3, first strand: chain 'L' and resid 215 through 217 removed outlier: 6.678A pdb=" N ILE L 216 " --> pdb=" O VAL L 224 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ALA L 225 " --> pdb=" O TRP L 244 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N TRP L 244 " --> pdb=" O ALA L 225 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL L 227 " --> pdb=" O VAL L 242 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL L 242 " --> pdb=" O VAL L 227 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'M' and resid 37 through 39 Processing sheet with id=AJ5, first strand: chain 'M' and resid 76 through 78 Processing sheet with id=AJ6, first strand: chain 'N' and resid 37 through 39 Processing sheet with id=AJ7, first strand: chain 'N' and resid 76 through 78 Processing sheet with id=AJ8, first strand: chain 'O' and resid 37 through 39 Processing sheet with id=AJ9, first strand: chain 'O' and resid 76 through 78 Processing sheet with id=AK1, first strand: chain 'P' and resid 37 through 39 Processing sheet with id=AK2, first strand: chain 'P' and resid 76 through 78 839 hydrogen bonds defined for protein. 2172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.55 Time building geometry restraints manager: 8.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10935 1.34 - 1.46: 7769 1.46 - 1.58: 15670 1.58 - 1.70: 2 1.70 - 1.83: 292 Bond restraints: 34668 Sorted by residual: bond pdb=" CB PRO F 183 " pdb=" CG PRO F 183 " ideal model delta sigma weight residual 1.492 1.631 -0.139 5.00e-02 4.00e+02 7.70e+00 bond pdb=" CA ALA J 5 " pdb=" C ALA J 5 " ideal model delta sigma weight residual 1.522 1.554 -0.033 1.24e-02 6.50e+03 6.90e+00 bond pdb=" N ALA H 40 " pdb=" CA ALA H 40 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.31e-02 5.83e+03 6.31e+00 bond pdb=" CB PRO D 22 " pdb=" CG PRO D 22 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.21e+00 bond pdb=" N ILE E 228 " pdb=" CA ILE E 228 " ideal model delta sigma weight residual 1.459 1.431 0.028 1.22e-02 6.72e+03 5.20e+00 ... (remaining 34663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 46433 2.66 - 5.31: 665 5.31 - 7.97: 95 7.97 - 10.63: 24 10.63 - 13.28: 7 Bond angle restraints: 47224 Sorted by residual: angle pdb=" O ILE K 228 " pdb=" C ILE K 228 " pdb=" N ASP K 229 " ideal model delta sigma weight residual 122.62 135.47 -12.85 1.40e+00 5.10e-01 8.42e+01 angle pdb=" CA ILE K 228 " pdb=" C ILE K 228 " pdb=" N ASP K 229 " ideal model delta sigma weight residual 116.45 103.17 13.28 1.46e+00 4.69e-01 8.28e+01 angle pdb=" N TYR G 93 " pdb=" CA TYR G 93 " pdb=" C TYR G 93 " ideal model delta sigma weight residual 111.36 120.79 -9.43 1.09e+00 8.42e-01 7.48e+01 angle pdb=" CA PRO F 183 " pdb=" N PRO F 183 " pdb=" CD PRO F 183 " ideal model delta sigma weight residual 112.00 100.56 11.44 1.40e+00 5.10e-01 6.68e+01 angle pdb=" N ALA J 310 " pdb=" CA ALA J 310 " pdb=" C ALA J 310 " ideal model delta sigma weight residual 110.23 120.69 -10.46 1.45e+00 4.76e-01 5.20e+01 ... (remaining 47219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 17840 18.02 - 36.04: 2236 36.04 - 54.06: 638 54.06 - 72.07: 123 72.07 - 90.09: 47 Dihedral angle restraints: 20884 sinusoidal: 8296 harmonic: 12588 Sorted by residual: dihedral pdb=" CB CYS J 63 " pdb=" SG CYS J 63 " pdb=" SG CYS J 96 " pdb=" CB CYS J 96 " ideal model delta sinusoidal sigma weight residual 93.00 6.61 86.39 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS M 72 " pdb=" SG CYS M 72 " pdb=" SG CYS M 84 " pdb=" CB CYS M 84 " ideal model delta sinusoidal sigma weight residual -86.00 -172.15 86.15 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 27 " pdb=" CB CYS B 27 " ideal model delta sinusoidal sigma weight residual -86.00 -171.89 85.89 1 1.00e+01 1.00e-02 8.91e+01 ... (remaining 20881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4399 0.067 - 0.133: 726 0.133 - 0.200: 68 0.200 - 0.266: 18 0.266 - 0.333: 9 Chirality restraints: 5220 Sorted by residual: chirality pdb=" CA TYR G 93 " pdb=" N TYR G 93 " pdb=" C TYR G 93 " pdb=" CB TYR G 93 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA ALA J 310 " pdb=" N ALA J 310 " pdb=" C ALA J 310 " pdb=" CB ALA J 310 " both_signs ideal model delta sigma weight residual False 2.48 2.15 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA GLU E 35 " pdb=" N GLU E 35 " pdb=" C GLU E 35 " pdb=" CB GLU E 35 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 5217 not shown) Planarity restraints: 6120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP E 348 " -0.077 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO E 349 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO E 349 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO E 349 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 21 " 0.074 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO D 22 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO D 22 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 22 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 309 " -0.021 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" C TYR A 309 " 0.071 2.00e-02 2.50e+03 pdb=" O TYR A 309 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA A 310 " -0.024 2.00e-02 2.50e+03 ... (remaining 6117 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 3 2.05 - 2.76: 4975 2.76 - 3.48: 41953 3.48 - 4.19: 73868 4.19 - 4.90: 130324 Nonbonded interactions: 251123 Sorted by model distance: nonbonded pdb=" OD1 ASP P 53 " pdb="CA CA P 201 " model vdw 1.341 2.510 nonbonded pdb=" CG ASP P 53 " pdb="CA CA P 201 " model vdw 1.961 2.740 nonbonded pdb=" OD2 ASP P 57 " pdb=" OD2 ASP P 63 " model vdw 2.023 3.040 nonbonded pdb=" OD1 ASP H 3 " pdb=" NZ LYS O 70 " model vdw 2.143 3.120 nonbonded pdb=" OD2 ASP O 96 " pdb="CA CA O 202 " model vdw 2.184 2.510 ... (remaining 251118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 1.270 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 72.070 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.220 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.474 34752 Z= 0.340 Angle : 0.853 43.523 47392 Z= 0.480 Chirality : 0.052 0.333 5220 Planarity : 0.007 0.116 6120 Dihedral : 17.182 90.093 12568 Min Nonbonded Distance : 1.341 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.19 % Allowed : 29.97 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.42 (0.11), residues: 4332 helix: -3.75 (0.13), residues: 376 sheet: -0.21 (0.17), residues: 1020 loop : -1.94 (0.10), residues: 2936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 142 HIS 0.006 0.001 HIS A 183 PHE 0.047 0.002 PHE A 437 TYR 0.013 0.001 TYR L 163 ARG 0.019 0.000 ARG G 143 Details of bonding type rmsd hydrogen bonds : bond 0.29557 ( 839) hydrogen bonds : angle 10.23057 ( 2172) SS BOND : bond 0.11631 ( 84) SS BOND : angle 5.38893 ( 168) covalent geometry : bond 0.00356 (34668) covalent geometry : angle 0.79215 (47224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 445 time to evaluate : 3.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.8367 (tt0) cc_final: 0.8099 (tt0) REVERT: B 199 CYS cc_start: 0.6012 (m) cc_final: 0.5767 (m) REVERT: B 219 ASP cc_start: 0.6436 (t0) cc_final: 0.6171 (t0) REVERT: G 35 ASN cc_start: 0.8650 (m110) cc_final: 0.8427 (m110) REVERT: G 51 TYR cc_start: 0.9076 (p90) cc_final: 0.8824 (p90) REVERT: G 164 ILE cc_start: 0.8977 (mm) cc_final: 0.8728 (mm) REVERT: G 397 GLU cc_start: 0.8089 (tp30) cc_final: 0.7720 (tt0) REVERT: H 64 TYR cc_start: 0.7724 (m-80) cc_final: 0.7441 (m-80) REVERT: J 10 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7663 (mmmt) REVERT: K 194 GLN cc_start: 0.7886 (mp10) cc_final: 0.7167 (tt0) REVERT: K 201 CYS cc_start: 0.4505 (OUTLIER) cc_final: 0.3714 (t) REVERT: L 211 ASP cc_start: 0.8431 (m-30) cc_final: 0.8043 (m-30) outliers start: 7 outliers final: 0 residues processed: 450 average time/residue: 0.4549 time to fit residues: 330.6079 Evaluate side-chains 380 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 3.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 201 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 20.0000 chunk 327 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 220 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 338 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 252 optimal weight: 8.9990 chunk 392 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 253 ASN B 5 HIS B 41 HIS B 168 GLN B 175 HIS ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 219 ASN E 168 GLN E 230 ASN E 253 HIS E 338 GLN E 391 ASN F 119 ASN ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 HIS F 194 GLN G 35 ASN G 226 GLN G 236 GLN G 328 ASN G 343 ASN G 369 GLN G 395 HIS H 168 GLN H 230 ASN H 404 GLN I 119 ASN J 35 ASN J 439 HIS K 126 HIS K 155 HIS K 222 GLN L 119 ASN M 39 GLN M 83 GLN N 83 GLN O 83 GLN P 83 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.165874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.124436 restraints weight = 43721.097| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.35 r_work: 0.3049 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 34752 Z= 0.195 Angle : 0.632 8.372 47392 Z= 0.335 Chirality : 0.047 0.251 5220 Planarity : 0.006 0.080 6120 Dihedral : 5.501 74.677 4705 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 5.13 % Allowed : 26.26 % Favored : 68.61 % 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: -1.96 (0.12), residues: 4332 helix: -1.39 (0.23), residues: 416 sheet: -0.37 (0.15), residues: 1148 loop : -1.78 (0.11), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 188 HIS 0.006 0.001 HIS J 125 PHE 0.023 0.002 PHE A 311 TYR 0.024 0.002 TYR A 309 ARG 0.006 0.001 ARG G 268 Details of bonding type rmsd hydrogen bonds : bond 0.05150 ( 839) hydrogen bonds : angle 6.53358 ( 2172) SS BOND : bond 0.00474 ( 84) SS BOND : angle 1.19935 ( 168) covalent geometry : bond 0.00466 (34668) covalent geometry : angle 0.62885 (47224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 392 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8655 (mmtp) REVERT: A 265 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6931 (tm-30) REVERT: A 313 PHE cc_start: 0.8065 (m-80) cc_final: 0.7678 (m-10) REVERT: B 174 ASP cc_start: 0.8471 (t0) cc_final: 0.8204 (t0) REVERT: B 219 ASP cc_start: 0.6560 (t0) cc_final: 0.6116 (t0) REVERT: D 226 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7574 (pp30) REVERT: D 265 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7436 (tp30) REVERT: D 309 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7178 (m-80) REVERT: D 422 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7306 (mm) REVERT: E 165 GLU cc_start: 0.8532 (tt0) cc_final: 0.8267 (tt0) REVERT: E 221 LYS cc_start: 0.8651 (mptt) cc_final: 0.7820 (mtmt) REVERT: E 305 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8563 (ttt-90) REVERT: F 236 ARG cc_start: 0.3167 (OUTLIER) cc_final: 0.2355 (mtm180) REVERT: G 51 TYR cc_start: 0.9118 (p90) cc_final: 0.8891 (p90) REVERT: G 164 ILE cc_start: 0.9029 (mm) cc_final: 0.8666 (mm) REVERT: G 397 GLU cc_start: 0.8467 (tp30) cc_final: 0.8228 (tt0) REVERT: H 64 TYR cc_start: 0.8105 (m-80) cc_final: 0.7687 (m-80) REVERT: H 205 ARG cc_start: 0.6785 (mtp85) cc_final: 0.6325 (mtm-85) REVERT: H 284 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9234 (mp) REVERT: H 292 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9031 (tp) REVERT: I 185 PHE cc_start: 0.5278 (OUTLIER) cc_final: 0.4999 (m-10) REVERT: J 414 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7205 (mp) REVERT: K 194 GLN cc_start: 0.7696 (mp10) cc_final: 0.7223 (mt0) REVERT: K 376 MET cc_start: 0.7952 (ttm) cc_final: 0.7700 (mmp) REVERT: M 53 ASP cc_start: 0.7601 (p0) cc_final: 0.7382 (p0) REVERT: N 51 LYS cc_start: 0.7494 (tttt) cc_final: 0.6821 (tptt) outliers start: 192 outliers final: 118 residues processed: 548 average time/residue: 0.4247 time to fit residues: 385.2483 Evaluate side-chains 496 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 367 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 292 LEU Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain J residue 423 VAL Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 294 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain P residue 63 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 164 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 271 optimal weight: 10.0000 chunk 297 optimal weight: 40.0000 chunk 192 optimal weight: 8.9990 chunk 165 optimal weight: 20.0000 chunk 200 optimal weight: 20.0000 chunk 424 optimal weight: 0.1980 chunk 218 optimal weight: 9.9990 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 GLN B 114 HIS ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 ASN ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 GLN H 155 HIS J 35 ASN K 168 GLN L 190 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.162042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.121360 restraints weight = 43774.088| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.43 r_work: 0.2967 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 34752 Z= 0.223 Angle : 0.656 9.179 47392 Z= 0.345 Chirality : 0.048 0.271 5220 Planarity : 0.005 0.071 6120 Dihedral : 5.671 78.002 4704 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 7.19 % Allowed : 24.30 % Favored : 68.50 % 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: -1.89 (0.12), residues: 4332 helix: -0.48 (0.26), residues: 416 sheet: -0.51 (0.16), residues: 1112 loop : -1.79 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 188 HIS 0.006 0.001 HIS J 125 PHE 0.013 0.002 PHE B 113 TYR 0.021 0.002 TYR A 309 ARG 0.005 0.000 ARG G 268 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 839) hydrogen bonds : angle 6.09466 ( 2172) SS BOND : bond 0.00352 ( 84) SS BOND : angle 1.65018 ( 168) covalent geometry : bond 0.00550 (34668) covalent geometry : angle 0.65013 (47224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 381 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8784 (tt) REVERT: A 54 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8143 (pttt) REVERT: A 123 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8641 (mmtp) REVERT: A 424 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7566 (tt) REVERT: C 259 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6664 (tp30) REVERT: D 19 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8508 (t) REVERT: D 99 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7875 (tm-30) REVERT: D 226 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7782 (pp30) REVERT: D 265 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7499 (tp30) REVERT: D 309 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: D 439 HIS cc_start: 0.7319 (OUTLIER) cc_final: 0.6714 (m170) REVERT: E 119 ARG cc_start: 0.8300 (mmm160) cc_final: 0.7829 (mmm160) REVERT: E 165 GLU cc_start: 0.8566 (tt0) cc_final: 0.8312 (tt0) REVERT: E 221 LYS cc_start: 0.8646 (mptt) cc_final: 0.7878 (mtmt) REVERT: E 305 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8587 (ttt-90) REVERT: E 362 LEU cc_start: 0.5510 (OUTLIER) cc_final: 0.5284 (pt) REVERT: F 236 ARG cc_start: 0.2968 (OUTLIER) cc_final: 0.2339 (mtm180) REVERT: G 44 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.8946 (tp) REVERT: G 397 GLU cc_start: 0.8458 (tp30) cc_final: 0.8242 (tt0) REVERT: H 64 TYR cc_start: 0.8215 (m-80) cc_final: 0.7807 (m-80) REVERT: H 205 ARG cc_start: 0.7294 (mtp85) cc_final: 0.6835 (mtm-85) REVERT: H 284 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9244 (mt) REVERT: H 292 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8930 (tp) REVERT: I 185 PHE cc_start: 0.5401 (OUTLIER) cc_final: 0.5072 (m-10) REVERT: K 168 GLN cc_start: 0.8571 (tt0) cc_final: 0.8290 (tt0) REVERT: K 194 GLN cc_start: 0.8020 (mp10) cc_final: 0.7189 (mt0) REVERT: K 229 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7030 (t0) REVERT: K 376 MET cc_start: 0.7900 (ttm) cc_final: 0.7583 (mmp) REVERT: L 200 PHE cc_start: 0.5346 (t80) cc_final: 0.5085 (t80) REVERT: M 53 ASP cc_start: 0.7596 (p0) cc_final: 0.7372 (p0) REVERT: N 51 LYS cc_start: 0.7706 (tttt) cc_final: 0.6989 (tptt) outliers start: 269 outliers final: 186 residues processed: 601 average time/residue: 0.4302 time to fit residues: 433.3996 Evaluate side-chains 572 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 368 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 223 CYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 152 ARG Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 292 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 423 VAL Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 229 ASP Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 294 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 108 CYS Chi-restraints excluded: chain P residue 53 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 260 optimal weight: 7.9990 chunk 274 optimal weight: 0.0570 chunk 317 optimal weight: 7.9990 chunk 289 optimal weight: 0.7980 chunk 182 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 368 optimal weight: 8.9990 chunk 259 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 356 HIS H 155 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.165419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.124314 restraints weight = 43931.090| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.38 r_work: 0.3028 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34752 Z= 0.122 Angle : 0.568 9.515 47392 Z= 0.296 Chirality : 0.044 0.220 5220 Planarity : 0.005 0.064 6120 Dihedral : 5.303 77.822 4704 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 5.21 % Allowed : 26.28 % Favored : 68.50 % 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: -1.68 (0.12), residues: 4332 helix: 0.04 (0.27), residues: 416 sheet: -0.44 (0.16), residues: 1124 loop : -1.67 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 188 HIS 0.006 0.001 HIS G 125 PHE 0.011 0.001 PHE J 353 TYR 0.013 0.001 TYR A 309 ARG 0.003 0.000 ARG H 388 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 839) hydrogen bonds : angle 5.67671 ( 2172) SS BOND : bond 0.00281 ( 84) SS BOND : angle 1.17840 ( 168) covalent geometry : bond 0.00293 (34668) covalent geometry : angle 0.56424 (47224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 390 time to evaluate : 3.983 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 54 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8159 (pttt) REVERT: A 123 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8675 (mmtp) REVERT: A 424 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7641 (tt) REVERT: B 305 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.8810 (ttm170) REVERT: C 259 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6526 (tp30) REVERT: D 99 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8107 (tm-30) REVERT: D 226 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7720 (pp30) REVERT: D 265 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7704 (tp30) REVERT: D 309 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.7279 (m-80) REVERT: D 382 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8137 (mmmt) REVERT: E 119 ARG cc_start: 0.8309 (mmm160) cc_final: 0.7787 (mmm160) REVERT: E 165 GLU cc_start: 0.8715 (tt0) cc_final: 0.8446 (tt0) REVERT: E 177 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7767 (pp) REVERT: E 305 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8609 (ttt-90) REVERT: E 362 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.5298 (pt) REVERT: E 376 MET cc_start: 0.7168 (tpt) cc_final: 0.6803 (tpt) REVERT: G 51 TYR cc_start: 0.9139 (p90) cc_final: 0.8920 (p90) REVERT: G 164 ILE cc_start: 0.9074 (mm) cc_final: 0.8714 (mm) REVERT: G 299 ASP cc_start: 0.7552 (m-30) cc_final: 0.7230 (t0) REVERT: G 397 GLU cc_start: 0.8665 (tp30) cc_final: 0.8384 (tt0) REVERT: G 400 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8805 (m) REVERT: H 31 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.8036 (tp) REVERT: H 64 TYR cc_start: 0.8343 (m-80) cc_final: 0.7924 (m-80) REVERT: H 205 ARG cc_start: 0.7322 (mtp85) cc_final: 0.6711 (mtm-85) REVERT: I 185 PHE cc_start: 0.5517 (OUTLIER) cc_final: 0.5205 (m-10) REVERT: K 177 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7023 (pp) REVERT: K 376 MET cc_start: 0.7835 (ttm) cc_final: 0.7429 (mmp) REVERT: L 200 PHE cc_start: 0.5385 (t80) cc_final: 0.5131 (t80) REVERT: M 53 ASP cc_start: 0.7748 (p0) cc_final: 0.7464 (p0) REVERT: N 51 LYS cc_start: 0.7744 (tttt) cc_final: 0.6937 (tptt) outliers start: 195 outliers final: 139 residues processed: 541 average time/residue: 0.4322 time to fit residues: 389.2823 Evaluate side-chains 526 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 372 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 359 THR Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 253 ASN Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 108 CYS Chi-restraints excluded: chain P residue 53 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 353 optimal weight: 10.0000 chunk 295 optimal weight: 8.9990 chunk 237 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 373 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 284 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 GLN H 155 HIS K 168 GLN L 121 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.161613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.120770 restraints weight = 43684.673| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.30 r_work: 0.2928 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 34752 Z= 0.261 Angle : 0.689 9.326 47392 Z= 0.360 Chirality : 0.049 0.226 5220 Planarity : 0.006 0.071 6120 Dihedral : 5.852 81.865 4704 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 7.70 % Allowed : 24.28 % Favored : 68.02 % 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: -1.81 (0.12), residues: 4332 helix: 0.26 (0.27), residues: 404 sheet: -0.62 (0.16), residues: 1108 loop : -1.76 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 188 HIS 0.008 0.001 HIS J 125 PHE 0.014 0.002 PHE A 87 TYR 0.021 0.002 TYR A 309 ARG 0.007 0.001 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 839) hydrogen bonds : angle 5.85922 ( 2172) SS BOND : bond 0.00398 ( 84) SS BOND : angle 1.67429 ( 168) covalent geometry : bond 0.00647 (34668) covalent geometry : angle 0.68289 (47224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 288 poor density : 385 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8789 (tt) REVERT: A 54 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8196 (pttt) REVERT: A 123 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8681 (mmtp) REVERT: A 424 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7519 (tt) REVERT: B 151 ASN cc_start: 0.9292 (OUTLIER) cc_final: 0.9065 (p0) REVERT: B 305 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.8762 (ttm170) REVERT: C 147 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6616 (pp30) REVERT: C 259 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6560 (tp30) REVERT: D 19 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8541 (t) REVERT: D 35 ASN cc_start: 0.8869 (m-40) cc_final: 0.8657 (m-40) REVERT: D 99 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7857 (tm-30) REVERT: D 226 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8209 (pt0) REVERT: D 265 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7812 (tp30) REVERT: D 309 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: D 422 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7320 (mm) REVERT: D 439 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6274 (m170) REVERT: E 119 ARG cc_start: 0.8466 (mmm160) cc_final: 0.7960 (mmm160) REVERT: E 165 GLU cc_start: 0.8763 (tt0) cc_final: 0.8479 (tt0) REVERT: E 177 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8194 (pp) REVERT: E 221 LYS cc_start: 0.8740 (mptt) cc_final: 0.7957 (mtmt) REVERT: E 300 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8407 (p0) REVERT: E 305 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8696 (ttt-90) REVERT: E 362 LEU cc_start: 0.5660 (OUTLIER) cc_final: 0.5427 (pt) REVERT: F 236 ARG cc_start: 0.2673 (OUTLIER) cc_final: 0.2071 (mtm180) REVERT: G 44 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.8951 (tp) REVERT: G 125 HIS cc_start: 0.5723 (OUTLIER) cc_final: 0.4180 (t-170) REVERT: G 130 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8258 (pt0) REVERT: G 152 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6340 (mp0) REVERT: G 164 ILE cc_start: 0.9056 (mm) cc_final: 0.8713 (mm) REVERT: G 268 ARG cc_start: 0.9482 (OUTLIER) cc_final: 0.8533 (ptp-170) REVERT: G 299 ASP cc_start: 0.7562 (m-30) cc_final: 0.7202 (t0) REVERT: G 397 GLU cc_start: 0.8711 (tp30) cc_final: 0.8447 (tt0) REVERT: H 64 TYR cc_start: 0.8292 (m-80) cc_final: 0.7796 (m-80) REVERT: H 205 ARG cc_start: 0.7534 (mtp85) cc_final: 0.7043 (mtm-85) REVERT: H 284 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9235 (mt) REVERT: I 185 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.5445 (m-10) REVERT: J 99 GLU cc_start: 0.7953 (pp20) cc_final: 0.7625 (pp20) REVERT: J 125 HIS cc_start: 0.5958 (OUTLIER) cc_final: 0.4798 (t-90) REVERT: K 197 TYR cc_start: 0.7383 (p90) cc_final: 0.7077 (p90) REVERT: K 376 MET cc_start: 0.7918 (ttm) cc_final: 0.7343 (mmp) REVERT: L 146 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7031 (mm-30) REVERT: M 53 ASP cc_start: 0.7429 (p0) cc_final: 0.7176 (p0) outliers start: 288 outliers final: 214 residues processed: 621 average time/residue: 0.4297 time to fit residues: 446.8803 Evaluate side-chains 615 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 373 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 156 LYS Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 268 ARG Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 253 ASN Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 423 VAL Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 294 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 108 CYS Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 63 ASP Chi-restraints excluded: chain P residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 233 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 426 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 383 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 362 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 85 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS J 176 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.161957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.121013 restraints weight = 43786.082| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.36 r_work: 0.2995 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34752 Z= 0.147 Angle : 0.593 8.491 47392 Z= 0.310 Chirality : 0.045 0.221 5220 Planarity : 0.005 0.086 6120 Dihedral : 5.523 82.023 4704 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 6.34 % Allowed : 25.78 % Favored : 67.89 % 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: -1.69 (0.12), residues: 4332 helix: 0.32 (0.27), residues: 416 sheet: -0.53 (0.16), residues: 1168 loop : -1.71 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 188 HIS 0.005 0.001 HIS G 125 PHE 0.014 0.001 PHE G 353 TYR 0.018 0.001 TYR G 137 ARG 0.005 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 839) hydrogen bonds : angle 5.56391 ( 2172) SS BOND : bond 0.00287 ( 84) SS BOND : angle 1.29038 ( 168) covalent geometry : bond 0.00359 (34668) covalent geometry : angle 0.58865 (47224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 386 time to evaluate : 3.680 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 54 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8225 (ptmt) REVERT: A 55 VAL cc_start: 0.9445 (OUTLIER) cc_final: 0.9204 (m) REVERT: A 123 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8678 (mmtp) REVERT: A 362 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8656 (mt) REVERT: B 305 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8793 (ttm170) REVERT: D 99 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7974 (tm-30) REVERT: D 226 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8031 (pt0) REVERT: D 265 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7808 (tp30) REVERT: D 309 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: D 439 HIS cc_start: 0.7194 (OUTLIER) cc_final: 0.6300 (m170) REVERT: E 119 ARG cc_start: 0.8490 (mmm160) cc_final: 0.8008 (mmm160) REVERT: E 157 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7312 (ptp90) REVERT: E 177 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8200 (pp) REVERT: E 221 LYS cc_start: 0.8794 (mptt) cc_final: 0.8027 (mtmt) REVERT: E 305 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8618 (ttt-90) REVERT: E 376 MET cc_start: 0.7215 (tpt) cc_final: 0.6823 (tpt) REVERT: G 44 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8913 (tp) REVERT: G 125 HIS cc_start: 0.5494 (OUTLIER) cc_final: 0.4128 (t-170) REVERT: G 130 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8359 (pt0) REVERT: G 164 ILE cc_start: 0.9021 (mm) cc_final: 0.8719 (mm) REVERT: G 268 ARG cc_start: 0.9440 (OUTLIER) cc_final: 0.8259 (ptp-170) REVERT: G 299 ASP cc_start: 0.7486 (m-30) cc_final: 0.7173 (t0) REVERT: G 397 GLU cc_start: 0.8704 (tp30) cc_final: 0.8432 (tt0) REVERT: H 64 TYR cc_start: 0.8357 (m-80) cc_final: 0.7943 (m-80) REVERT: H 205 ARG cc_start: 0.7540 (mtp85) cc_final: 0.7063 (mtm-85) REVERT: H 284 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9235 (mt) REVERT: I 185 PHE cc_start: 0.5747 (OUTLIER) cc_final: 0.5323 (m-10) REVERT: J 99 GLU cc_start: 0.7834 (pp20) cc_final: 0.7221 (pp20) REVERT: J 125 HIS cc_start: 0.5555 (OUTLIER) cc_final: 0.4480 (t-90) REVERT: K 114 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7186 (m90) REVERT: K 177 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7084 (pp) REVERT: K 200 LYS cc_start: 0.7709 (tppp) cc_final: 0.7154 (tptt) REVERT: K 376 MET cc_start: 0.8005 (ttm) cc_final: 0.7417 (mmp) REVERT: L 125 TYR cc_start: 0.8088 (m-80) cc_final: 0.7821 (m-80) REVERT: L 146 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7101 (mm-30) REVERT: L 200 PHE cc_start: 0.5480 (t80) cc_final: 0.5172 (t80) REVERT: M 53 ASP cc_start: 0.7549 (p0) cc_final: 0.7253 (p0) outliers start: 237 outliers final: 189 residues processed: 572 average time/residue: 0.4302 time to fit residues: 409.8637 Evaluate side-chains 592 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 381 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 156 LYS Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 268 ARG Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 418 THR Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 253 ASN Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 108 CYS Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 231 optimal weight: 5.9990 chunk 195 optimal weight: 20.0000 chunk 429 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 249 optimal weight: 0.9990 chunk 348 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 353 optimal weight: 10.0000 chunk 364 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS J 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.161840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.121099 restraints weight = 43803.300| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.38 r_work: 0.2990 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34752 Z= 0.153 Angle : 0.588 8.081 47392 Z= 0.307 Chirality : 0.046 0.226 5220 Planarity : 0.005 0.080 6120 Dihedral : 5.436 82.140 4704 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 6.95 % Allowed : 25.08 % Favored : 67.97 % 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: -1.67 (0.12), residues: 4332 helix: 0.41 (0.27), residues: 420 sheet: -0.49 (0.16), residues: 1112 loop : -1.70 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 188 HIS 0.005 0.001 HIS G 125 PHE 0.011 0.001 PHE G 353 TYR 0.017 0.001 TYR G 137 ARG 0.007 0.000 ARG G 143 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 839) hydrogen bonds : angle 5.46364 ( 2172) SS BOND : bond 0.00283 ( 84) SS BOND : angle 1.14683 ( 168) covalent geometry : bond 0.00376 (34668) covalent geometry : angle 0.58485 (47224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 382 time to evaluate : 4.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8240 (ptmt) REVERT: A 95 PHE cc_start: 0.7911 (t80) cc_final: 0.7576 (t80) REVERT: A 123 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8693 (mmtp) REVERT: A 362 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8669 (mt) REVERT: B 305 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.8793 (ttm170) REVERT: C 147 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6585 (pp30) REVERT: D 19 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8606 (t) REVERT: D 99 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7966 (tm-30) REVERT: D 226 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7835 (pp30) REVERT: D 265 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7816 (tp30) REVERT: D 306 GLU cc_start: 0.7676 (tp30) cc_final: 0.7293 (tt0) REVERT: D 309 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: D 349 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: D 439 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6390 (m170) REVERT: E 119 ARG cc_start: 0.8426 (mmm160) cc_final: 0.7956 (mmm160) REVERT: E 157 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7339 (ptp90) REVERT: E 177 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8195 (pp) REVERT: E 305 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8593 (ttt-90) REVERT: E 362 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5489 (pt) REVERT: G 44 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9004 (tp) REVERT: G 125 HIS cc_start: 0.5415 (OUTLIER) cc_final: 0.4071 (t-170) REVERT: G 130 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8355 (pt0) REVERT: G 164 ILE cc_start: 0.9023 (mm) cc_final: 0.8717 (mm) REVERT: G 268 ARG cc_start: 0.9431 (OUTLIER) cc_final: 0.8262 (ptp-170) REVERT: G 299 ASP cc_start: 0.7495 (m-30) cc_final: 0.7183 (t0) REVERT: G 397 GLU cc_start: 0.8697 (tp30) cc_final: 0.8431 (tt0) REVERT: H 64 TYR cc_start: 0.8332 (m-80) cc_final: 0.7950 (m-80) REVERT: H 205 ARG cc_start: 0.7496 (mtp85) cc_final: 0.7086 (mtm-85) REVERT: H 284 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9235 (mt) REVERT: I 185 PHE cc_start: 0.5771 (OUTLIER) cc_final: 0.5398 (m-10) REVERT: J 99 GLU cc_start: 0.7827 (pp20) cc_final: 0.7484 (pp20) REVERT: J 125 HIS cc_start: 0.5470 (OUTLIER) cc_final: 0.4503 (t-90) REVERT: K 177 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7064 (pp) REVERT: K 200 LYS cc_start: 0.7630 (tppp) cc_final: 0.7163 (tptt) REVERT: K 229 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.6920 (t0) REVERT: K 376 MET cc_start: 0.7992 (ttm) cc_final: 0.7411 (mmp) REVERT: L 200 PHE cc_start: 0.5469 (t80) cc_final: 0.5181 (t80) REVERT: M 53 ASP cc_start: 0.7558 (p0) cc_final: 0.7250 (p0) outliers start: 260 outliers final: 210 residues processed: 585 average time/residue: 0.4207 time to fit residues: 411.6218 Evaluate side-chains 609 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 375 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 41 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 156 LYS Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 268 ARG Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 418 THR Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 253 ASN Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 309 TYR Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 229 ASP Chi-restraints excluded: chain K residue 233 TRP Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain L residue 117 MET Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 108 CYS Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 325 optimal weight: 0.3980 chunk 226 optimal weight: 4.9990 chunk 260 optimal weight: 0.0980 chunk 159 optimal weight: 5.9990 chunk 378 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 335 optimal weight: 4.9990 chunk 293 optimal weight: 40.0000 chunk 107 optimal weight: 20.0000 chunk 127 optimal weight: 0.0370 chunk 315 optimal weight: 7.9990 overall best weight: 1.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN B 358 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS J 176 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.164543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.123103 restraints weight = 43587.112| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.20 r_work: 0.2985 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34752 Z= 0.108 Angle : 0.554 9.768 47392 Z= 0.288 Chirality : 0.044 0.242 5220 Planarity : 0.004 0.067 6120 Dihedral : 5.147 81.079 4704 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.72 % Allowed : 26.26 % Favored : 68.02 % 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: -1.52 (0.12), residues: 4332 helix: 0.61 (0.27), residues: 420 sheet: -0.35 (0.16), residues: 1108 loop : -1.63 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 188 HIS 0.006 0.001 HIS B 24 PHE 0.015 0.001 PHE A 437 TYR 0.016 0.001 TYR G 137 ARG 0.006 0.000 ARG G 143 Details of bonding type rmsd hydrogen bonds : bond 0.03218 ( 839) hydrogen bonds : angle 5.26037 ( 2172) SS BOND : bond 0.00262 ( 84) SS BOND : angle 1.10961 ( 168) covalent geometry : bond 0.00257 (34668) covalent geometry : angle 0.55060 (47224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 401 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.7868 (t80) cc_final: 0.7573 (t80) REVERT: A 123 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8581 (mmtp) REVERT: B 19 CYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7512 (t) REVERT: B 31 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8234 (tt) REVERT: B 305 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8781 (ttm170) REVERT: C 147 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6420 (pp30) REVERT: D 19 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8527 (t) REVERT: D 99 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8001 (tm-30) REVERT: D 226 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7752 (pp30) REVERT: D 265 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7751 (tp30) REVERT: D 309 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7307 (m-10) REVERT: D 439 HIS cc_start: 0.7104 (OUTLIER) cc_final: 0.6270 (m170) REVERT: E 119 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8014 (mmm160) REVERT: E 157 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7327 (ptp90) REVERT: E 177 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7997 (pp) REVERT: E 305 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8545 (ttt-90) REVERT: G 44 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8910 (tp) REVERT: G 164 ILE cc_start: 0.9034 (mm) cc_final: 0.8724 (mm) REVERT: G 268 ARG cc_start: 0.9397 (OUTLIER) cc_final: 0.8132 (ptp-170) REVERT: G 299 ASP cc_start: 0.7503 (m-30) cc_final: 0.7187 (t0) REVERT: G 397 GLU cc_start: 0.8673 (tp30) cc_final: 0.8424 (tt0) REVERT: H 31 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.7926 (tp) REVERT: H 64 TYR cc_start: 0.8324 (m-80) cc_final: 0.7960 (m-80) REVERT: H 284 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9194 (mt) REVERT: I 185 PHE cc_start: 0.5800 (OUTLIER) cc_final: 0.5434 (m-10) REVERT: J 99 GLU cc_start: 0.7736 (pp20) cc_final: 0.6870 (pp20) REVERT: J 125 HIS cc_start: 0.5355 (OUTLIER) cc_final: 0.4450 (t-90) REVERT: K 114 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7040 (m90) REVERT: K 177 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6973 (pp) REVERT: K 200 LYS cc_start: 0.7402 (tppp) cc_final: 0.7044 (tptt) REVERT: K 229 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.6706 (t0) REVERT: K 376 MET cc_start: 0.8047 (ttm) cc_final: 0.7483 (mmp) REVERT: L 125 TYR cc_start: 0.8112 (m-80) cc_final: 0.7822 (m-80) REVERT: L 200 PHE cc_start: 0.5442 (t80) cc_final: 0.5163 (t80) REVERT: M 53 ASP cc_start: 0.7525 (p0) cc_final: 0.7196 (p0) outliers start: 214 outliers final: 163 residues processed: 568 average time/residue: 0.4183 time to fit residues: 393.7291 Evaluate side-chains 566 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 381 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 268 ARG Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 418 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 253 ASN Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 229 ASP Chi-restraints excluded: chain K residue 233 TRP 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 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 163 TYR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 108 CYS Chi-restraints excluded: chain P residue 63 ASP Chi-restraints excluded: chain P residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 146 optimal weight: 20.0000 chunk 204 optimal weight: 20.0000 chunk 363 optimal weight: 9.9990 chunk 310 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 94 optimal weight: 30.0000 chunk 73 optimal weight: 0.9990 chunk 406 optimal weight: 0.6980 chunk 231 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS J 176 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.163065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.122087 restraints weight = 43936.747| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.35 r_work: 0.3021 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34752 Z= 0.134 Angle : 0.575 12.009 47392 Z= 0.298 Chirality : 0.045 0.270 5220 Planarity : 0.005 0.064 6120 Dihedral : 5.188 81.095 4704 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 5.78 % Allowed : 26.42 % Favored : 67.81 % 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: -1.48 (0.12), residues: 4332 helix: 0.85 (0.27), residues: 408 sheet: -0.30 (0.16), residues: 1068 loop : -1.62 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 188 HIS 0.005 0.001 HIS G 125 PHE 0.010 0.001 PHE J 399 TYR 0.015 0.001 TYR A 309 ARG 0.007 0.000 ARG G 143 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 839) hydrogen bonds : angle 5.25295 ( 2172) SS BOND : bond 0.00252 ( 84) SS BOND : angle 1.41819 ( 168) covalent geometry : bond 0.00327 (34668) covalent geometry : angle 0.56943 (47224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 384 time to evaluate : 3.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8663 (mmtp) REVERT: B 19 CYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7796 (t) REVERT: B 31 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8268 (tt) REVERT: B 305 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8835 (ttm170) REVERT: C 147 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6450 (pp30) REVERT: C 259 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7073 (pm20) REVERT: D 19 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8525 (t) REVERT: D 99 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7983 (tm-30) REVERT: D 226 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7778 (pp30) REVERT: D 265 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7746 (tp30) REVERT: D 309 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7349 (m-10) REVERT: D 439 HIS cc_start: 0.7109 (OUTLIER) cc_final: 0.6295 (m170) REVERT: E 119 ARG cc_start: 0.8409 (mmm160) cc_final: 0.7976 (mmm160) REVERT: E 157 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7325 (ptp90) REVERT: E 177 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8073 (pp) REVERT: E 305 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8588 (ttt-90) REVERT: G 164 ILE cc_start: 0.9025 (mm) cc_final: 0.8717 (mm) REVERT: G 268 ARG cc_start: 0.9411 (OUTLIER) cc_final: 0.8262 (ptp-170) REVERT: G 299 ASP cc_start: 0.7493 (m-30) cc_final: 0.7197 (t0) REVERT: G 397 GLU cc_start: 0.8709 (tp30) cc_final: 0.8451 (tt0) REVERT: G 408 TRP cc_start: 0.7983 (OUTLIER) cc_final: 0.7148 (t60) REVERT: H 31 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8202 (tp) REVERT: H 205 ARG cc_start: 0.7250 (mtp85) cc_final: 0.6896 (mtm-85) REVERT: H 284 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9213 (mt) REVERT: I 185 PHE cc_start: 0.5760 (OUTLIER) cc_final: 0.5371 (m-10) REVERT: J 125 HIS cc_start: 0.5429 (OUTLIER) cc_final: 0.4492 (t-90) REVERT: J 322 LYS cc_start: 0.9018 (ptpt) cc_final: 0.8640 (pttt) REVERT: K 114 HIS cc_start: 0.8067 (OUTLIER) cc_final: 0.7057 (m90) REVERT: K 177 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7035 (pp) REVERT: K 197 TYR cc_start: 0.7547 (p90) cc_final: 0.7222 (p90) REVERT: K 200 LYS cc_start: 0.7455 (tppp) cc_final: 0.7221 (tptt) REVERT: K 229 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.6761 (t0) REVERT: K 376 MET cc_start: 0.8002 (ttm) cc_final: 0.7426 (mmp) REVERT: L 125 TYR cc_start: 0.8084 (m-80) cc_final: 0.7785 (m-80) REVERT: L 200 PHE cc_start: 0.5317 (t80) cc_final: 0.5022 (t80) REVERT: M 53 ASP cc_start: 0.7505 (p0) cc_final: 0.7155 (p0) outliers start: 216 outliers final: 181 residues processed: 552 average time/residue: 0.4347 time to fit residues: 399.0705 Evaluate side-chains 582 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 378 time to evaluate : 3.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 268 ARG Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 408 TRP Chi-restraints excluded: chain G residue 418 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 253 ASN Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 229 ASP Chi-restraints excluded: chain K residue 233 TRP Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 163 TYR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 108 CYS Chi-restraints excluded: chain P residue 63 ASP Chi-restraints excluded: chain P residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 289 optimal weight: 40.0000 chunk 177 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 129 optimal weight: 0.0870 chunk 368 optimal weight: 40.0000 chunk 376 optimal weight: 2.9990 chunk 336 optimal weight: 0.8980 chunk 356 optimal weight: 10.0000 chunk 338 optimal weight: 3.9990 chunk 284 optimal weight: 8.9990 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN B 168 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS J 176 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.162761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.121580 restraints weight = 43735.332| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.26 r_work: 0.3019 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34752 Z= 0.152 Angle : 0.589 9.199 47392 Z= 0.306 Chirality : 0.046 0.265 5220 Planarity : 0.005 0.063 6120 Dihedral : 5.274 81.503 4704 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 5.78 % Allowed : 26.42 % Favored : 67.81 % 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: -1.49 (0.12), residues: 4332 helix: 0.84 (0.27), residues: 408 sheet: -0.31 (0.16), residues: 1068 loop : -1.63 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 188 HIS 0.005 0.001 HIS G 125 PHE 0.011 0.001 PHE J 355 TYR 0.017 0.001 TYR A 309 ARG 0.010 0.000 ARG G 143 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 839) hydrogen bonds : angle 5.28641 ( 2172) SS BOND : bond 0.00276 ( 84) SS BOND : angle 1.33743 ( 168) covalent geometry : bond 0.00373 (34668) covalent geometry : angle 0.58456 (47224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 381 time to evaluate : 4.545 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 29 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8830 (tt) REVERT: A 123 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8680 (mmtp) REVERT: B 19 CYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7519 (t) REVERT: B 31 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8260 (tt) REVERT: B 151 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8976 (p0) REVERT: B 213 HIS cc_start: 0.7858 (t-90) cc_final: 0.7531 (t70) REVERT: B 305 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8780 (ttm170) REVERT: C 147 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6450 (pp30) REVERT: C 259 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7037 (pm20) REVERT: D 19 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8548 (t) REVERT: D 99 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7983 (tm-30) REVERT: D 226 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7808 (pp30) REVERT: D 309 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7414 (m-80) REVERT: D 349 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7575 (mm-30) REVERT: D 439 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6377 (m170) REVERT: E 119 ARG cc_start: 0.8378 (mmm160) cc_final: 0.7900 (mmm160) REVERT: E 157 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7325 (ptp90) REVERT: E 177 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8168 (pp) REVERT: E 305 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8575 (ttt-90) REVERT: G 164 ILE cc_start: 0.9037 (mm) cc_final: 0.8734 (mm) REVERT: G 268 ARG cc_start: 0.9424 (OUTLIER) cc_final: 0.8331 (ptp-170) REVERT: G 299 ASP cc_start: 0.7474 (m-30) cc_final: 0.7182 (t0) REVERT: G 397 GLU cc_start: 0.8701 (tp30) cc_final: 0.8442 (tt0) REVERT: G 408 TRP cc_start: 0.7980 (OUTLIER) cc_final: 0.7052 (t60) REVERT: H 205 ARG cc_start: 0.7292 (mtp85) cc_final: 0.6906 (mtm-85) REVERT: H 284 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9216 (mt) REVERT: I 185 PHE cc_start: 0.5802 (OUTLIER) cc_final: 0.5400 (m-10) REVERT: J 125 HIS cc_start: 0.5548 (OUTLIER) cc_final: 0.4543 (t-90) REVERT: J 322 LYS cc_start: 0.9125 (ptpt) cc_final: 0.8629 (pttt) REVERT: K 114 HIS cc_start: 0.8030 (OUTLIER) cc_final: 0.6981 (m90) REVERT: K 177 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7055 (pp) REVERT: K 197 TYR cc_start: 0.7483 (p90) cc_final: 0.7088 (p90) REVERT: K 200 LYS cc_start: 0.7377 (tppp) cc_final: 0.7043 (tptt) REVERT: K 229 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.6785 (t0) REVERT: K 376 MET cc_start: 0.7979 (ttm) cc_final: 0.7403 (mmp) REVERT: L 125 TYR cc_start: 0.8103 (m-80) cc_final: 0.7788 (m-80) REVERT: L 146 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7027 (mm-30) REVERT: L 200 PHE cc_start: 0.5255 (t80) cc_final: 0.4952 (t80) outliers start: 216 outliers final: 181 residues processed: 549 average time/residue: 0.5341 time to fit residues: 488.6552 Evaluate side-chains 582 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 376 time to evaluate : 5.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 ARG Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 268 ARG Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 408 TRP Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 223 CYS Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 253 ASN Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 370 VAL Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 217 CYS Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 229 ASP Chi-restraints excluded: chain K residue 233 TRP Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 365 ILE Chi-restraints excluded: chain K residue 371 CYS Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain L residue 135 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 163 TYR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 188 TRP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 108 CYS Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 63 ASP Chi-restraints excluded: chain P residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 204 optimal weight: 1.9990 chunk 294 optimal weight: 30.0000 chunk 147 optimal weight: 0.0270 chunk 209 optimal weight: 9.9990 chunk 335 optimal weight: 1.9990 chunk 324 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS J 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.163241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.122374 restraints weight = 43810.169| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.34 r_work: 0.3022 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34752 Z= 0.129 Angle : 0.573 8.876 47392 Z= 0.298 Chirality : 0.045 0.256 5220 Planarity : 0.005 0.062 6120 Dihedral : 5.178 80.694 4704 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 5.64 % Allowed : 26.50 % Favored : 67.86 % 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: -1.48 (0.12), residues: 4332 helix: 0.72 (0.27), residues: 420 sheet: -0.28 (0.17), residues: 1068 loop : -1.61 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 188 HIS 0.005 0.001 HIS G 125 PHE 0.010 0.001 PHE J 353 TYR 0.015 0.001 TYR G 137 ARG 0.008 0.000 ARG G 143 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 839) hydrogen bonds : angle 5.20511 ( 2172) SS BOND : bond 0.00253 ( 84) SS BOND : angle 1.22288 ( 168) covalent geometry : bond 0.00314 (34668) covalent geometry : angle 0.56948 (47224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22384.66 seconds wall clock time: 389 minutes 1.67 seconds (23341.67 seconds total)