Starting phenix.real_space_refine on Mon May 26 04:02:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zvi_60511/05_2025/8zvi_60511.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zvi_60511/05_2025/8zvi_60511.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/8zvi_60511/05_2025/8zvi_60511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zvi_60511/05_2025/8zvi_60511.map" model { file = "/net/cci-nas-00/data/ceres_data/8zvi_60511/05_2025/8zvi_60511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zvi_60511/05_2025/8zvi_60511.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 ------------------------------------------------------------------------------- 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= 0.014 sd= 2.129 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 18166 2.51 5 N 4832 2.21 5 O 5570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28628 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "B" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "C" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "D" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "E" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "F" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "G" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2281 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 7, 'TRANS': 286} Chain: "H" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "I" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "J" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2281 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 7, 'TRANS': 286} Chain: "K" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2281 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 7, 'TRANS': 286} Chain: "L" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2281 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 7, 'TRANS': 286} Chain: "a" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 532 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "b" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 532 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Time building chain proxies: 16.66, per 1000 atoms: 0.58 Number of scatterers: 28628 At special positions: 0 Unit cell: (201.5, 292.5, 88.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 5570 8.00 N 4832 7.00 C 18166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 7.56 Conformation dependent library (CDL) restraints added in 3.8 seconds 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6896 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 69 sheets defined 29.0% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'A' and resid 191 through 196 removed outlier: 3.790A pdb=" N LEU A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 191 through 196' Processing helix chain 'A' and resid 257 through 263 removed outlier: 3.628A pdb=" N GLU A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 289 removed outlier: 3.735A pdb=" N ARG A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 273 " --> pdb=" O PRO A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 4.435A pdb=" N SER A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.532A pdb=" N ILE A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.965A pdb=" N LEU A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 335' Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 350 through 353 Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.893A pdb=" N THR B 231 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 267 through 289 removed outlier: 3.505A pdb=" N LEU B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 323 through 329 Processing helix chain 'B' and resid 330 through 335 removed outlier: 4.112A pdb=" N LEU B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 335' Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.577A pdb=" N LEU B 339 " --> pdb=" O ARG B 336 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS B 340 " --> pdb=" O HIS B 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 336 through 340' Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.792A pdb=" N LEU C 195 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHE C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 196' Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.948A pdb=" N THR C 231 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 267 through 289 removed outlier: 3.520A pdb=" N ILE C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 4.030A pdb=" N SER C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 330 removed outlier: 3.534A pdb=" N ILE C 327 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 330 " --> pdb=" O THR C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 341 removed outlier: 6.538A pdb=" N ARG C 336 " --> pdb=" O LYS C 333 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS C 337 " --> pdb=" O LEU C 334 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 339 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS C 340 " --> pdb=" O HIS C 337 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 341 " --> pdb=" O GLY C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'D' and resid 191 through 196 removed outlier: 3.790A pdb=" N LEU D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N PHE D 196 " --> pdb=" O VAL D 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 191 through 196' Processing helix chain 'D' and resid 257 through 263 removed outlier: 3.629A pdb=" N GLU D 261 " --> pdb=" O ASP D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 289 removed outlier: 3.644A pdb=" N ARG D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 4.158A pdb=" N SER D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 330 removed outlier: 3.537A pdb=" N ILE D 327 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 328 " --> pdb=" O ALA D 324 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 330 " --> pdb=" O THR D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 341 removed outlier: 6.600A pdb=" N ARG D 336 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N HIS D 337 " --> pdb=" O LEU D 334 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS D 340 " --> pdb=" O HIS D 337 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 341 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 353 Processing helix chain 'D' and resid 372 through 377 Processing helix chain 'D' and resid 407 through 409 No H-bonds generated for 'chain 'D' and resid 407 through 409' Processing helix chain 'E' and resid 171 through 174 Processing helix chain 'E' and resid 227 through 231 removed outlier: 3.678A pdb=" N THR E 231 " --> pdb=" O ASP E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 263 Processing helix chain 'E' and resid 267 through 290 removed outlier: 3.751A pdb=" N LEU E 271 " --> pdb=" O LEU E 267 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 305 Processing helix chain 'E' and resid 324 through 329 Processing helix chain 'E' and resid 330 through 339 removed outlier: 6.714A pdb=" N ARG E 336 " --> pdb=" O LYS E 333 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS E 337 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU E 339 " --> pdb=" O ARG E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 353 Processing helix chain 'E' and resid 372 through 377 Processing helix chain 'E' and resid 407 through 409 No H-bonds generated for 'chain 'E' and resid 407 through 409' Processing helix chain 'F' and resid 227 through 231 removed outlier: 3.684A pdb=" N THR F 231 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 263 Processing helix chain 'F' and resid 267 through 289 Processing helix chain 'F' and resid 298 through 305 Processing helix chain 'F' and resid 323 through 330 removed outlier: 3.669A pdb=" N LEU F 330 " --> pdb=" O THR F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 339 removed outlier: 6.606A pdb=" N ARG F 336 " --> pdb=" O LYS F 333 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N HIS F 337 " --> pdb=" O LEU F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 358 removed outlier: 3.862A pdb=" N ASP F 355 " --> pdb=" O ASP F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 377 Processing helix chain 'G' and resid 191 through 196 removed outlier: 3.790A pdb=" N LEU G 195 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE G 196 " --> pdb=" O VAL G 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 191 through 196' Processing helix chain 'G' and resid 257 through 263 Processing helix chain 'G' and resid 267 through 289 Processing helix chain 'G' and resid 298 through 306 removed outlier: 4.158A pdb=" N SER G 304 " --> pdb=" O LEU G 300 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 330 removed outlier: 3.536A pdb=" N ILE G 327 " --> pdb=" O THR G 323 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER G 328 " --> pdb=" O ALA G 324 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU G 330 " --> pdb=" O THR G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 335 removed outlier: 3.825A pdb=" N LEU G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY G 335 " --> pdb=" O ARG G 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 330 through 335' Processing helix chain 'G' and resid 336 through 339 Processing helix chain 'G' and resid 350 through 353 Processing helix chain 'G' and resid 372 through 377 Processing helix chain 'G' and resid 407 through 409 No H-bonds generated for 'chain 'G' and resid 407 through 409' Processing helix chain 'H' and resid 171 through 174 Processing helix chain 'H' and resid 191 through 196 removed outlier: 3.762A pdb=" N LEU H 195 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE H 196 " --> pdb=" O VAL H 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 191 through 196' Processing helix chain 'H' and resid 227 through 232 Processing helix chain 'H' and resid 257 through 262 Processing helix chain 'H' and resid 267 through 289 removed outlier: 3.560A pdb=" N LEU H 271 " --> pdb=" O LEU H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 306 removed outlier: 3.925A pdb=" N SER H 304 " --> pdb=" O LEU H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 330 removed outlier: 3.629A pdb=" N LEU H 330 " --> pdb=" O THR H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 333 No H-bonds generated for 'chain 'H' and resid 331 through 333' Processing helix chain 'H' and resid 334 through 341 removed outlier: 4.054A pdb=" N HIS H 337 " --> pdb=" O LEU H 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU H 339 " --> pdb=" O ARG H 336 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS H 340 " --> pdb=" O HIS H 337 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU H 341 " --> pdb=" O GLY H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 353 Processing helix chain 'H' and resid 359 through 363 removed outlier: 3.757A pdb=" N GLN H 363 " --> pdb=" O GLU H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 377 Processing helix chain 'H' and resid 407 through 409 No H-bonds generated for 'chain 'H' and resid 407 through 409' Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 191 through 196 removed outlier: 3.887A pdb=" N LEU I 195 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE I 196 " --> pdb=" O VAL I 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 191 through 196' Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.545A pdb=" N THR I 231 " --> pdb=" O ASP I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 263 Processing helix chain 'I' and resid 267 through 289 Processing helix chain 'I' and resid 298 through 306 Processing helix chain 'I' and resid 323 through 335 removed outlier: 3.583A pdb=" N ILE I 327 " --> pdb=" O THR I 323 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU I 330 " --> pdb=" O THR I 326 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG I 331 " --> pdb=" O ILE I 327 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG I 332 " --> pdb=" O SER I 328 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS I 333 " --> pdb=" O LYS I 329 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU I 334 " --> pdb=" O LEU I 330 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY I 335 " --> pdb=" O ARG I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 341 removed outlier: 4.172A pdb=" N LYS I 340 " --> pdb=" O HIS I 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU I 341 " --> pdb=" O GLY I 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 337 through 341' Processing helix chain 'I' and resid 350 through 353 Processing helix chain 'I' and resid 359 through 363 removed outlier: 3.822A pdb=" N GLN I 363 " --> pdb=" O GLU I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 377 Processing helix chain 'J' and resid 227 through 232 removed outlier: 3.865A pdb=" N THR J 231 " --> pdb=" O ASP J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 263 Processing helix chain 'J' and resid 267 through 290 Processing helix chain 'J' and resid 298 through 306 Processing helix chain 'J' and resid 323 through 330 removed outlier: 3.561A pdb=" N ILE J 327 " --> pdb=" O THR J 323 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU J 330 " --> pdb=" O THR J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 330 through 335 removed outlier: 3.923A pdb=" N LEU J 334 " --> pdb=" O LEU J 330 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY J 335 " --> pdb=" O ARG J 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 330 through 335' Processing helix chain 'J' and resid 336 through 341 removed outlier: 3.656A pdb=" N LEU J 339 " --> pdb=" O ARG J 336 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS J 340 " --> pdb=" O HIS J 337 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU J 341 " --> pdb=" O GLY J 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 336 through 341' Processing helix chain 'J' and resid 349 through 353 Processing helix chain 'J' and resid 372 through 377 Processing helix chain 'J' and resid 407 through 409 No H-bonds generated for 'chain 'J' and resid 407 through 409' Processing helix chain 'K' and resid 191 through 196 removed outlier: 3.792A pdb=" N LEU K 195 " --> pdb=" O VAL K 191 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHE K 196 " --> pdb=" O VAL K 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 191 through 196' Processing helix chain 'K' and resid 257 through 263 removed outlier: 3.628A pdb=" N GLU K 261 " --> pdb=" O ASP K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 289 removed outlier: 3.562A pdb=" N LEU K 271 " --> pdb=" O LEU K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 306 Processing helix chain 'K' and resid 323 through 329 Processing helix chain 'K' and resid 330 through 335 removed outlier: 4.177A pdb=" N LEU K 334 " --> pdb=" O LEU K 330 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY K 335 " --> pdb=" O ARG K 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 330 through 335' Processing helix chain 'K' and resid 336 through 338 No H-bonds generated for 'chain 'K' and resid 336 through 338' Processing helix chain 'K' and resid 349 through 358 Processing helix chain 'K' and resid 359 through 363 Processing helix chain 'K' and resid 372 through 377 Processing helix chain 'K' and resid 407 through 409 No H-bonds generated for 'chain 'K' and resid 407 through 409' Processing helix chain 'L' and resid 227 through 231 removed outlier: 3.547A pdb=" N THR L 230 " --> pdb=" O THR L 227 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR L 231 " --> pdb=" O ASP L 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 227 through 231' Processing helix chain 'L' and resid 256 through 263 Processing helix chain 'L' and resid 267 through 289 Processing helix chain 'L' and resid 298 through 306 Processing helix chain 'L' and resid 323 through 330 removed outlier: 3.535A pdb=" N ILE L 327 " --> pdb=" O THR L 323 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER L 328 " --> pdb=" O ALA L 324 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU L 330 " --> pdb=" O THR L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 331 through 341 removed outlier: 6.536A pdb=" N ARG L 336 " --> pdb=" O LYS L 333 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS L 337 " --> pdb=" O LEU L 334 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU L 339 " --> pdb=" O ARG L 336 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS L 340 " --> pdb=" O HIS L 337 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU L 341 " --> pdb=" O GLY L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 353 Processing helix chain 'L' and resid 372 through 377 Processing helix chain 'L' and resid 407 through 409 No H-bonds generated for 'chain 'L' and resid 407 through 409' Processing helix chain 'a' and resid 3 through 11 removed outlier: 4.088A pdb=" N THR a 9 " --> pdb=" O SER a 5 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE a 10 " --> pdb=" O GLY a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 22 removed outlier: 3.613A pdb=" N PHE a 22 " --> pdb=" O SER a 18 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 25 No H-bonds generated for 'chain 'a' and resid 23 through 25' Processing helix chain 'a' and resid 26 through 31 removed outlier: 4.595A pdb=" N TYR a 30 " --> pdb=" O ALA a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 32 through 42 removed outlier: 4.056A pdb=" N PHE a 36 " --> pdb=" O PRO a 32 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU a 37 " --> pdb=" O SER a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 64 removed outlier: 3.655A pdb=" N ILE a 64 " --> pdb=" O TYR a 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 11 removed outlier: 3.840A pdb=" N THR b 9 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE b 10 " --> pdb=" O GLY b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 24 Processing helix chain 'b' and resid 24 through 31 removed outlier: 4.085A pdb=" N LYS b 29 " --> pdb=" O VAL b 25 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR b 30 " --> pdb=" O ALA b 26 " (cutoff:3.500A) Processing helix chain 'b' and resid 32 through 42 removed outlier: 3.724A pdb=" N PHE b 36 " --> pdb=" O PRO b 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 48 through 64 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 197 through 199 removed outlier: 6.648A pdb=" N GLU A 197 " --> pdb=" O MET A 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 241 removed outlier: 5.843A pdb=" N THR A 207 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG F 181 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE F 183 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 218 through 220 removed outlier: 4.349A pdb=" N LYS F 248 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 248 through 256 removed outlier: 3.512A pdb=" N ALA A 433 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 437 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 420 " --> pdb=" O THR A 437 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG A 439 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA A 418 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 309 through 311 removed outlier: 6.055A pdb=" N SER A 452 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY A 453 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU A 401 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 381 through 382 Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 177 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 177 Processing sheet with id=AB2, first strand: chain 'B' and resid 197 through 200 removed outlier: 6.638A pdb=" N GLU B 197 " --> pdb=" O MET B 413 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ARG B 415 " --> pdb=" O GLU B 197 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU B 199 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ARG B 417 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ALA B 418 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG B 439 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 443 through 444 removed outlier: 5.267A pdb=" N ALA B 418 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG B 439 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU C 233 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS B 252 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 309 through 315 removed outlier: 6.949A pdb=" N ALA B 314 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA B 403 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR B 455 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU B 401 " --> pdb=" O TYR B 455 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE B 402 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU B 344 " --> pdb=" O PRO B 386 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N VAL B 388 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 346 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N SER B 390 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL B 348 " --> pdb=" O SER B 390 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 182 through 183 Processing sheet with id=AB6, first strand: chain 'C' and resid 197 through 199 removed outlier: 4.161A pdb=" N GLU C 197 " --> pdb=" O PHE C 411 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 417 through 426 removed outlier: 6.039A pdb=" N ALA C 418 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG C 439 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 420 " --> pdb=" O THR C 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 437 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 433 " --> pdb=" O GLU C 424 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP C 432 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS C 248 " --> pdb=" O VAL D 220 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 417 through 426 removed outlier: 6.039A pdb=" N ALA C 418 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG C 439 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 420 " --> pdb=" O THR C 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 437 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 433 " --> pdb=" O GLU C 424 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP C 432 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU D 233 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS C 252 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 309 through 311 removed outlier: 6.056A pdb=" N SER C 452 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY C 453 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 401 " --> pdb=" O GLY C 453 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE C 402 " --> pdb=" O SER C 349 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL C 348 " --> pdb=" O SER C 390 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 381 through 382 Processing sheet with id=AC2, first strand: chain 'D' and resid 176 through 177 Processing sheet with id=AC3, first strand: chain 'D' and resid 182 through 183 Processing sheet with id=AC4, first strand: chain 'D' and resid 197 through 199 removed outlier: 6.648A pdb=" N GLU D 197 " --> pdb=" O MET D 413 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 248 through 256 removed outlier: 3.512A pdb=" N ALA D 433 " --> pdb=" O GLU D 424 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 437 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 420 " --> pdb=" O THR D 437 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ARG D 439 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ALA D 418 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 310 through 311 removed outlier: 6.755A pdb=" N VAL D 310 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 403 " --> pdb=" O GLY D 453 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 381 through 382 Processing sheet with id=AC8, first strand: chain 'E' and resid 176 through 177 Processing sheet with id=AC9, first strand: chain 'E' and resid 182 through 183 Processing sheet with id=AD1, first strand: chain 'E' and resid 197 through 199 removed outlier: 6.818A pdb=" N GLU E 197 " --> pdb=" O MET E 413 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 247 through 256 removed outlier: 3.582A pdb=" N TYR E 247 " --> pdb=" O VAL E 440 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ARG E 439 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ALA E 418 " --> pdb=" O ARG E 439 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 309 through 315 removed outlier: 3.505A pdb=" N ALA E 456 " --> pdb=" O THR E 312 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA E 314 " --> pdb=" O ALA E 456 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 388 through 389 Processing sheet with id=AD5, first strand: chain 'E' and resid 381 through 382 Processing sheet with id=AD6, first strand: chain 'F' and resid 197 through 199 removed outlier: 6.732A pdb=" N GLU F 197 " --> pdb=" O MET F 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'F' and resid 309 through 315 removed outlier: 3.653A pdb=" N ALA F 456 " --> pdb=" O THR F 312 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA F 314 " --> pdb=" O ALA F 456 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA F 403 " --> pdb=" O GLY F 453 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU F 346 " --> pdb=" O VAL F 388 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N SER F 390 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL F 348 " --> pdb=" O SER F 390 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 177 through 183 removed outlier: 3.723A pdb=" N THR H 207 " --> pdb=" O ILE G 177 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU H 209 " --> pdb=" O SER G 179 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ARG G 181 " --> pdb=" O LEU H 209 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 197 through 199 removed outlier: 6.648A pdb=" N GLU G 197 " --> pdb=" O MET G 413 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 209 through 210 Processing sheet with id=AE2, first strand: chain 'G' and resid 218 through 220 removed outlier: 4.288A pdb=" N LYS L 248 " --> pdb=" O VAL G 220 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU G 233 " --> pdb=" O LYS L 252 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N PHE L 254 " --> pdb=" O GLU G 233 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 218 through 220 removed outlier: 4.288A pdb=" N LYS L 248 " --> pdb=" O VAL G 220 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN L 438 " --> pdb=" O LEU L 249 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA L 433 " --> pdb=" O GLU L 424 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR L 437 " --> pdb=" O THR L 420 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR L 420 " --> pdb=" O THR L 437 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG L 439 " --> pdb=" O ALA L 418 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ALA L 418 " --> pdb=" O ARG L 439 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 417 through 426 removed outlier: 5.937A pdb=" N ALA G 418 " --> pdb=" O ARG G 439 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG G 439 " --> pdb=" O ALA G 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR G 420 " --> pdb=" O THR G 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR G 437 " --> pdb=" O THR G 420 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA G 433 " --> pdb=" O GLU G 424 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS G 248 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 309 through 311 removed outlier: 6.054A pdb=" N SER G 452 " --> pdb=" O VAL G 310 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY G 453 " --> pdb=" O GLU G 401 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU G 401 " --> pdb=" O GLY G 453 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 381 through 382 Processing sheet with id=AE7, first strand: chain 'H' and resid 176 through 183 removed outlier: 4.362A pdb=" N LEU I 209 " --> pdb=" O SER H 179 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ARG H 181 " --> pdb=" O LEU I 209 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 197 through 199 removed outlier: 6.647A pdb=" N GLU H 197 " --> pdb=" O MET H 413 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 417 through 426 removed outlier: 5.938A pdb=" N ALA H 418 " --> pdb=" O ARG H 439 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG H 439 " --> pdb=" O ALA H 418 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR H 420 " --> pdb=" O THR H 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR H 437 " --> pdb=" O THR H 420 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA H 433 " --> pdb=" O GLU H 424 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP H 432 " --> pdb=" O ILE H 255 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE H 255 " --> pdb=" O ASP H 432 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR H 434 " --> pdb=" O SER H 253 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER H 253 " --> pdb=" O TYR H 434 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL H 436 " --> pdb=" O ALA H 251 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 251 " --> pdb=" O VAL H 436 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS H 248 " --> pdb=" O VAL I 220 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 417 through 426 removed outlier: 5.938A pdb=" N ALA H 418 " --> pdb=" O ARG H 439 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG H 439 " --> pdb=" O ALA H 418 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR H 420 " --> pdb=" O THR H 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR H 437 " --> pdb=" O THR H 420 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA H 433 " --> pdb=" O GLU H 424 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP H 432 " --> pdb=" O ILE H 255 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE H 255 " --> pdb=" O ASP H 432 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR H 434 " --> pdb=" O SER H 253 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER H 253 " --> pdb=" O TYR H 434 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL H 436 " --> pdb=" O ALA H 251 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 251 " --> pdb=" O VAL H 436 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU I 233 " --> pdb=" O ALA H 250 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS H 252 " --> pdb=" O GLU I 233 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 309 through 315 removed outlier: 3.509A pdb=" N ALA H 456 " --> pdb=" O THR H 312 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA H 314 " --> pdb=" O ALA H 456 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA H 403 " --> pdb=" O GLY H 453 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 381 through 382 Processing sheet with id=AF4, first strand: chain 'I' and resid 176 through 177 Processing sheet with id=AF5, first strand: chain 'I' and resid 182 through 183 Processing sheet with id=AF6, first strand: chain 'I' and resid 197 through 199 removed outlier: 4.002A pdb=" N GLU I 197 " --> pdb=" O PHE I 411 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 417 through 426 removed outlier: 6.145A pdb=" N ALA I 418 " --> pdb=" O ARG I 439 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ARG I 439 " --> pdb=" O ALA I 418 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR I 420 " --> pdb=" O THR I 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR I 437 " --> pdb=" O THR I 420 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA I 433 " --> pdb=" O GLU I 424 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL I 440 " --> pdb=" O TYR I 247 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU J 233 " --> pdb=" O ALA I 250 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS I 252 " --> pdb=" O GLU J 233 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 309 through 311 removed outlier: 3.847A pdb=" N ALA I 403 " --> pdb=" O GLY I 453 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL I 345 " --> pdb=" O VAL I 406 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 381 through 382 Processing sheet with id=AG1, first strand: chain 'J' and resid 182 through 183 Processing sheet with id=AG2, first strand: chain 'J' and resid 197 through 199 removed outlier: 6.649A pdb=" N GLU J 197 " --> pdb=" O MET J 413 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL J 412 " --> pdb=" O GLN J 443 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 417 through 426 removed outlier: 5.936A pdb=" N ALA J 418 " --> pdb=" O ARG J 439 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG J 439 " --> pdb=" O ALA J 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR J 420 " --> pdb=" O THR J 437 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR J 437 " --> pdb=" O THR J 420 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA J 433 " --> pdb=" O GLU J 424 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS J 248 " --> pdb=" O VAL K 220 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 417 through 426 removed outlier: 5.936A pdb=" N ALA J 418 " --> pdb=" O ARG J 439 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG J 439 " --> pdb=" O ALA J 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR J 420 " --> pdb=" O THR J 437 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR J 437 " --> pdb=" O THR J 420 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA J 433 " --> pdb=" O GLU J 424 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N GLU K 233 " --> pdb=" O LYS J 248 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ALA J 250 " --> pdb=" O GLU K 233 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 309 through 315 removed outlier: 6.918A pdb=" N ALA J 314 " --> pdb=" O ALA J 456 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY J 453 " --> pdb=" O PHE J 402 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR J 455 " --> pdb=" O ALA J 400 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ALA J 400 " --> pdb=" O TYR J 455 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 347 through 348 Processing sheet with id=AG7, first strand: chain 'J' and resid 381 through 382 Processing sheet with id=AG8, first strand: chain 'K' and resid 178 through 183 removed outlier: 5.798A pdb=" N THR L 207 " --> pdb=" O SER K 179 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG K 181 " --> pdb=" O THR L 207 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 197 through 199 removed outlier: 6.649A pdb=" N GLU K 197 " --> pdb=" O MET K 413 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 248 through 256 removed outlier: 3.512A pdb=" N ALA K 433 " --> pdb=" O GLU K 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR K 437 " --> pdb=" O THR K 420 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR K 420 " --> pdb=" O THR K 437 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG K 439 " --> pdb=" O ALA K 418 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ALA K 418 " --> pdb=" O ARG K 439 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 309 through 315 removed outlier: 7.051A pdb=" N ALA K 314 " --> pdb=" O ALA K 456 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA K 403 " --> pdb=" O GLY K 453 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR K 455 " --> pdb=" O GLU K 401 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU K 401 " --> pdb=" O TYR K 455 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 381 through 382 Processing sheet with id=AH4, first strand: chain 'L' and resid 197 through 199 removed outlier: 6.648A pdb=" N GLU L 197 " --> pdb=" O MET L 413 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 309 through 311 removed outlier: 6.055A pdb=" N SER L 452 " --> pdb=" O VAL L 310 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY L 453 " --> pdb=" O GLU L 401 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU L 401 " --> pdb=" O GLY L 453 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 381 through 382 885 hydrogen bonds defined for protein. 2268 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: 10.85 Time building geometry restraints manager: 8.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4892 1.28 - 1.41: 7105 1.41 - 1.54: 16905 1.54 - 1.67: 60 1.67 - 1.80: 120 Bond restraints: 29082 Sorted by residual: bond pdb=" CA LYS F 325 " pdb=" C LYS F 325 " ideal model delta sigma weight residual 1.524 1.396 0.128 1.29e-02 6.01e+03 9.82e+01 bond pdb=" CA SER C 179 " pdb=" C SER C 179 " ideal model delta sigma weight residual 1.524 1.410 0.114 1.27e-02 6.20e+03 8.12e+01 bond pdb=" CA ALA F 366 " pdb=" C ALA F 366 " ideal model delta sigma weight residual 1.523 1.409 0.115 1.28e-02 6.10e+03 8.01e+01 bond pdb=" CA ALA E 366 " pdb=" C ALA E 366 " ideal model delta sigma weight residual 1.521 1.433 0.088 9.90e-03 1.02e+04 7.89e+01 bond pdb=" CA TYR F 353 " pdb=" C TYR F 353 " ideal model delta sigma weight residual 1.524 1.411 0.112 1.27e-02 6.20e+03 7.81e+01 ... (remaining 29077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 34201 3.27 - 6.54: 4011 6.54 - 9.82: 891 9.82 - 13.09: 183 13.09 - 16.36: 22 Bond angle restraints: 39308 Sorted by residual: angle pdb=" N LYS B 340 " pdb=" CA LYS B 340 " pdb=" C LYS B 340 " ideal model delta sigma weight residual 111.07 124.32 -13.25 1.07e+00 8.73e-01 1.53e+02 angle pdb=" N LEU G 356 " pdb=" CA LEU G 356 " pdb=" C LEU G 356 " ideal model delta sigma weight residual 113.41 98.44 14.97 1.22e+00 6.72e-01 1.51e+02 angle pdb=" N LEU I 356 " pdb=" CA LEU I 356 " pdb=" C LEU I 356 " ideal model delta sigma weight residual 113.41 98.45 14.96 1.22e+00 6.72e-01 1.50e+02 angle pdb=" N LEU B 356 " pdb=" CA LEU B 356 " pdb=" C LEU B 356 " ideal model delta sigma weight residual 113.41 98.49 14.92 1.22e+00 6.72e-01 1.50e+02 angle pdb=" N LEU D 356 " pdb=" CA LEU D 356 " pdb=" C LEU D 356 " ideal model delta sigma weight residual 113.41 98.52 14.89 1.22e+00 6.72e-01 1.49e+02 ... (remaining 39303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 15009 17.17 - 34.34: 1719 34.34 - 51.51: 666 51.51 - 68.68: 252 68.68 - 85.85: 12 Dihedral angle restraints: 17658 sinusoidal: 6940 harmonic: 10718 Sorted by residual: dihedral pdb=" C SER K 173 " pdb=" N SER K 173 " pdb=" CA SER K 173 " pdb=" CB SER K 173 " ideal model delta harmonic sigma weight residual -122.60 -143.96 21.36 0 2.50e+00 1.60e-01 7.30e+01 dihedral pdb=" C SER G 173 " pdb=" N SER G 173 " pdb=" CA SER G 173 " pdb=" CB SER G 173 " ideal model delta harmonic sigma weight residual -122.60 -143.92 21.32 0 2.50e+00 1.60e-01 7.28e+01 dihedral pdb=" N SER K 173 " pdb=" C SER K 173 " pdb=" CA SER K 173 " pdb=" CB SER K 173 " ideal model delta harmonic sigma weight residual 122.80 143.42 -20.62 0 2.50e+00 1.60e-01 6.80e+01 ... (remaining 17655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 3489 0.175 - 0.349: 848 0.349 - 0.524: 193 0.524 - 0.698: 29 0.698 - 0.873: 9 Chirality restraints: 4568 Sorted by residual: chirality pdb=" CA SER K 173 " pdb=" N SER K 173 " pdb=" C SER K 173 " pdb=" CB SER K 173 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.90e+01 chirality pdb=" CA SER G 173 " pdb=" N SER G 173 " pdb=" C SER G 173 " pdb=" CB SER G 173 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.89e+01 chirality pdb=" CA GLU I 258 " pdb=" N GLU I 258 " pdb=" C GLU I 258 " pdb=" CB GLU I 258 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.81e+01 ... (remaining 4565 not shown) Planarity restraints: 5000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA K 263 " -0.027 2.00e-02 2.50e+03 5.35e-02 2.86e+01 pdb=" C ALA K 263 " 0.093 2.00e-02 2.50e+03 pdb=" O ALA K 263 " -0.035 2.00e-02 2.50e+03 pdb=" N ILE K 264 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 284 " 0.025 2.00e-02 2.50e+03 5.13e-02 2.64e+01 pdb=" CD GLU E 284 " -0.089 2.00e-02 2.50e+03 pdb=" OE1 GLU E 284 " 0.032 2.00e-02 2.50e+03 pdb=" OE2 GLU E 284 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 415 " 0.025 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C ARG E 415 " -0.087 2.00e-02 2.50e+03 pdb=" O ARG E 415 " 0.032 2.00e-02 2.50e+03 pdb=" N GLN E 416 " 0.030 2.00e-02 2.50e+03 ... (remaining 4997 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 7826 2.74 - 3.28: 25691 3.28 - 3.82: 47479 3.82 - 4.36: 59433 4.36 - 4.90: 98964 Nonbonded interactions: 239393 Sorted by model distance: nonbonded pdb=" O GLN K 376 " pdb=" CA GLY L 384 " model vdw 2.203 3.440 nonbonded pdb=" N ALA F 366 " pdb=" N GLN F 367 " model vdw 2.238 2.560 nonbonded pdb=" N PHE C 446 " pdb=" O PHE C 446 " model vdw 2.240 2.496 nonbonded pdb=" CG TYR C 354 " pdb=" CG ARG D 332 " model vdw 2.248 3.660 nonbonded pdb=" NE2 GLN D 378 " pdb=" CD1 LEU E 341 " model vdw 2.255 3.540 ... (remaining 239388 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 164 through 457) selection = (chain 'B' and resid 164 through 457) selection = (chain 'C' and resid 164 through 457) selection = (chain 'D' and resid 164 through 457) selection = (chain 'E' and resid 164 through 457) selection = (chain 'F' and resid 164 through 457) selection = chain 'G' selection = (chain 'H' and resid 164 through 457) selection = (chain 'I' and resid 164 through 457) selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' } 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 64.200 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.025 0.128 29082 Z= 1.802 Angle : 2.404 16.361 39308 Z= 1.620 Chirality : 0.167 0.873 4568 Planarity : 0.011 0.106 5000 Dihedral : 18.104 85.854 10762 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 23.98 Ramachandran Plot: Outliers : 2.11 % Allowed : 7.85 % Favored : 90.04 % Rotamer: Outliers : 21.79 % Allowed : 11.87 % Favored : 66.34 % Cbeta Deviations : 5.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 3656 helix: -0.13 (0.18), residues: 823 sheet: -1.02 (0.18), residues: 849 loop : -1.41 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP I 219 HIS 0.015 0.003 HIS I 243 PHE 0.033 0.004 PHE a 36 TYR 0.039 0.004 TYR J 445 ARG 0.012 0.002 ARG B 415 Details of bonding type rmsd hydrogen bonds : bond 0.25126 ( 830) hydrogen bonds : angle 9.26576 ( 2268) covalent geometry : bond 0.02458 (29082) covalent geometry : angle 2.40379 (39308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1778 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 672 poor density : 1106 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8288 (t) REVERT: A 229 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8331 (p) REVERT: A 236 LYS cc_start: 0.7306 (pttt) cc_final: 0.7005 (tptt) REVERT: A 295 LYS cc_start: 0.8832 (mttt) cc_final: 0.8617 (mttm) REVERT: A 333 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8193 (tptt) REVERT: A 346 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8125 (tt) REVERT: A 363 GLN cc_start: 0.8547 (mt0) cc_final: 0.7900 (mt0) REVERT: A 413 MET cc_start: 0.9060 (mtp) cc_final: 0.8795 (mtm) REVERT: A 422 GLU cc_start: 0.6320 (tt0) cc_final: 0.6021 (tt0) REVERT: A 429 LYS cc_start: 0.7252 (mtmt) cc_final: 0.6982 (tptp) REVERT: A 450 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8699 (t) REVERT: B 205 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8340 (mt) REVERT: B 264 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.6367 (mp) REVERT: B 288 MET cc_start: 0.8652 (mmt) cc_final: 0.7609 (mmt) REVERT: B 289 THR cc_start: 0.8987 (p) cc_final: 0.8748 (p) REVERT: B 317 ASP cc_start: 0.6292 (p0) cc_final: 0.5914 (p0) REVERT: B 383 TYR cc_start: 0.8199 (m-80) cc_final: 0.7429 (m-80) REVERT: B 405 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8308 (mt) REVERT: B 430 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: B 446 PHE cc_start: 0.7491 (m-80) cc_final: 0.7268 (m-80) REVERT: C 165 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8556 (m) REVERT: C 175 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7301 (mt-10) REVERT: C 177 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7953 (pt) REVERT: C 180 GLN cc_start: 0.7526 (mt0) cc_final: 0.7151 (mt0) REVERT: C 210 VAL cc_start: 0.9356 (t) cc_final: 0.9145 (t) REVERT: C 213 ASP cc_start: 0.7273 (m-30) cc_final: 0.7070 (m-30) REVERT: C 258 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: C 288 MET cc_start: 0.8215 (mmt) cc_final: 0.7761 (mmt) REVERT: D 269 PRO cc_start: 0.7602 (Cg_exo) cc_final: 0.7342 (Cg_endo) REVERT: D 359 ASP cc_start: 0.7663 (t0) cc_final: 0.7370 (t0) REVERT: D 362 TRP cc_start: 0.8762 (OUTLIER) cc_final: 0.7512 (m-90) REVERT: D 398 ASN cc_start: 0.7805 (m-40) cc_final: 0.7443 (m-40) REVERT: D 430 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7229 (mt0) REVERT: E 167 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8308 (p) REVERT: E 192 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8821 (m) REVERT: E 203 SER cc_start: 0.9005 (t) cc_final: 0.8746 (t) REVERT: E 430 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8512 (mm110) REVERT: F 168 GLU cc_start: 0.7258 (pt0) cc_final: 0.7043 (pt0) REVERT: F 187 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6692 (mm-40) REVERT: F 218 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8825 (p) REVERT: F 269 PRO cc_start: 0.9248 (OUTLIER) cc_final: 0.8765 (Cg_endo) REVERT: F 289 THR cc_start: 0.9057 (m) cc_final: 0.8845 (p) REVERT: F 346 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8854 (tp) REVERT: F 362 TRP cc_start: 0.8981 (OUTLIER) cc_final: 0.8312 (m-90) REVERT: F 372 SER cc_start: 0.7601 (OUTLIER) cc_final: 0.7360 (p) REVERT: F 382 ILE cc_start: 0.8957 (mm) cc_final: 0.8632 (pt) REVERT: F 420 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8574 (p) REVERT: F 426 GLN cc_start: 0.8076 (mt0) cc_final: 0.7721 (mt0) REVERT: F 450 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8677 (m) REVERT: G 167 VAL cc_start: 0.6864 (OUTLIER) cc_final: 0.6317 (t) REVERT: G 182 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8709 (mt) REVERT: G 255 ILE cc_start: 0.8403 (tt) cc_final: 0.8057 (tt) REVERT: G 312 THR cc_start: 0.7671 (p) cc_final: 0.7171 (t) REVERT: G 364 ASP cc_start: 0.7949 (m-30) cc_final: 0.7662 (m-30) REVERT: G 412 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8074 (m) REVERT: G 430 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.5273 (mp10) REVERT: H 310 VAL cc_start: 0.8756 (t) cc_final: 0.8393 (t) REVERT: H 311 VAL cc_start: 0.8793 (t) cc_final: 0.8585 (t) REVERT: H 351 ASP cc_start: 0.7169 (t0) cc_final: 0.6902 (t0) REVERT: H 363 GLN cc_start: 0.7892 (mt0) cc_final: 0.7448 (mt0) REVERT: H 399 SER cc_start: 0.8472 (m) cc_final: 0.8003 (t) REVERT: H 413 MET cc_start: 0.8487 (mtp) cc_final: 0.8183 (mtp) REVERT: H 441 ASN cc_start: 0.8149 (t0) cc_final: 0.7764 (t0) REVERT: H 442 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7926 (tt) REVERT: I 227 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8168 (p) REVERT: I 231 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8358 (p) REVERT: I 242 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8682 (pt) REVERT: I 252 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8320 (ptmt) REVERT: I 362 TRP cc_start: 0.8532 (OUTLIER) cc_final: 0.7391 (m-90) REVERT: I 398 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8744 (m-40) REVERT: I 410 ASN cc_start: 0.8605 (t0) cc_final: 0.8281 (t0) REVERT: I 430 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8183 (mt0) REVERT: J 208 MET cc_start: 0.8656 (mtp) cc_final: 0.8421 (mtt) REVERT: J 213 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6699 (p0) REVERT: J 229 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8764 (p) REVERT: J 240 LYS cc_start: 0.8627 (mttt) cc_final: 0.8420 (mtpp) REVERT: J 311 VAL cc_start: 0.8894 (t) cc_final: 0.8649 (p) REVERT: J 399 SER cc_start: 0.7801 (m) cc_final: 0.7213 (t) REVERT: J 444 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6988 (ptp-170) REVERT: K 172 GLU cc_start: -0.0205 (OUTLIER) cc_final: -0.0679 (tt0) REVERT: K 186 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6142 (tm) REVERT: K 270 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7444 (tm) REVERT: K 272 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6392 (tpp-160) REVERT: K 289 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.7937 (p) REVERT: L 168 GLU cc_start: 0.5458 (mt-10) cc_final: 0.5217 (mt-10) REVERT: L 175 GLU cc_start: 0.5601 (OUTLIER) cc_final: 0.2457 (mt-10) REVERT: L 183 ILE cc_start: 0.5801 (OUTLIER) cc_final: 0.5378 (pt) REVERT: L 209 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5604 (mt) REVERT: L 236 LYS cc_start: 0.7202 (pttt) cc_final: 0.5934 (tppt) REVERT: L 273 LYS cc_start: 0.7468 (mtpt) cc_final: 0.7225 (mmtt) REVERT: L 372 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.7827 (p) REVERT: a 60 TYR cc_start: 0.8185 (t80) cc_final: 0.7480 (t80) outliers start: 672 outliers final: 193 residues processed: 1511 average time/residue: 0.4252 time to fit residues: 994.7403 Evaluate side-chains 949 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 708 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 444 ARG Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 269 PRO Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 296 PRO Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 296 PRO Chi-restraints excluded: chain D residue 362 TRP Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 430 GLN Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 188 LYS Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 269 PRO Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 378 GLN Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 430 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 269 PRO Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 296 PRO Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 378 GLN Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 448 ASN Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain G residue 306 ASP Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 448 ASN Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 253 SER Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 270 LEU Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 296 PRO Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 349 SER Chi-restraints excluded: chain H residue 375 LEU Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain H residue 442 LEU Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 188 LYS Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 229 THR Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain I residue 242 ILE Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 269 PRO Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 398 ASN Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 450 VAL Chi-restraints excluded: chain I residue 454 THR Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 269 PRO Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 296 PRO Chi-restraints excluded: chain J residue 304 SER Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 375 LEU Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain J residue 444 ARG Chi-restraints excluded: chain J residue 454 THR Chi-restraints excluded: chain K residue 172 GLU Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 231 THR Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 262 ASP Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 327 ILE Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 412 VAL Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 444 ARG Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 182 ILE Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 209 LEU Chi-restraints excluded: chain L residue 372 SER Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain a residue 20 ILE Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 64 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 326 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 180 GLN ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN B 187 GLN B 279 HIS B 426 GLN B 438 GLN B 443 GLN B 448 ASN C 337 HIS ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 HIS D 363 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 GLN E 367 GLN E 378 GLN E 438 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 GLN F 416 GLN ** F 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 HIS ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 ASN H 162 ASN H 416 GLN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 ASN I 163 GLN I 243 HIS I 367 GLN I 438 GLN I 448 ASN J 367 GLN ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 438 GLN L 367 GLN L 378 GLN a 47 HIS ** b 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 49 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.119899 restraints weight = 40975.382| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.03 r_work: 0.3190 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 29082 Z= 0.237 Angle : 0.777 10.490 39308 Z= 0.423 Chirality : 0.049 0.358 4568 Planarity : 0.006 0.078 5000 Dihedral : 11.305 86.383 4425 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.21 % Favored : 93.03 % Rotamer: Outliers : 9.60 % Allowed : 19.36 % Favored : 71.04 % 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: -1.61 (0.13), residues: 3656 helix: -0.26 (0.18), residues: 785 sheet: -0.97 (0.17), residues: 916 loop : -1.43 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 219 HIS 0.012 0.002 HIS D 279 PHE 0.019 0.002 PHE F 244 TYR 0.033 0.002 TYR E 392 ARG 0.008 0.001 ARG L 336 Details of bonding type rmsd hydrogen bonds : bond 0.04811 ( 830) hydrogen bonds : angle 6.64032 ( 2268) covalent geometry : bond 0.00527 (29082) covalent geometry : angle 0.77699 (39308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 296 poor density : 776 time to evaluate : 3.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7542 (mt-10) REVERT: A 175 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 322 VAL cc_start: 0.8953 (t) cc_final: 0.8745 (t) REVERT: A 363 GLN cc_start: 0.8311 (mt0) cc_final: 0.8068 (mt0) REVERT: A 382 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8741 (pt) REVERT: A 413 MET cc_start: 0.9047 (mtp) cc_final: 0.8707 (mtm) REVERT: A 422 GLU cc_start: 0.6673 (tt0) cc_final: 0.6350 (tt0) REVERT: A 429 LYS cc_start: 0.7677 (mtmt) cc_final: 0.6924 (tptt) REVERT: B 186 LEU cc_start: 0.8257 (mt) cc_final: 0.7924 (mt) REVERT: B 204 LYS cc_start: 0.8063 (mtpt) cc_final: 0.7273 (mptt) REVERT: B 240 LYS cc_start: 0.8639 (mttt) cc_final: 0.8293 (mttt) REVERT: B 266 SER cc_start: 0.8426 (m) cc_final: 0.8009 (t) REVERT: B 267 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7710 (tp) REVERT: B 289 THR cc_start: 0.8682 (p) cc_final: 0.8399 (p) REVERT: B 346 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8612 (tp) REVERT: B 364 ASP cc_start: 0.6809 (OUTLIER) cc_final: 0.6510 (t0) REVERT: B 413 MET cc_start: 0.8115 (mtp) cc_final: 0.7875 (mtp) REVERT: B 430 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.6516 (mp10) REVERT: C 213 ASP cc_start: 0.7637 (m-30) cc_final: 0.7416 (m-30) REVERT: C 277 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: D 197 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7689 (mt-10) REVERT: D 284 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8072 (tm-30) REVERT: D 288 MET cc_start: 0.9204 (mmm) cc_final: 0.8751 (mmt) REVERT: D 351 ASP cc_start: 0.8106 (t70) cc_final: 0.7794 (t0) REVERT: D 358 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7513 (mt-10) REVERT: D 362 TRP cc_start: 0.9066 (OUTLIER) cc_final: 0.7904 (m-90) REVERT: D 392 TYR cc_start: 0.8189 (m-80) cc_final: 0.7857 (m-80) REVERT: D 420 THR cc_start: 0.8585 (p) cc_final: 0.8283 (p) REVERT: D 450 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8517 (t) REVERT: E 197 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7417 (mm-30) REVERT: F 181 ARG cc_start: 0.8133 (mtp180) cc_final: 0.7921 (mtp85) REVERT: F 185 ASP cc_start: 0.6788 (OUTLIER) cc_final: 0.6262 (t0) REVERT: F 311 VAL cc_start: 0.9175 (t) cc_final: 0.8944 (m) REVERT: F 346 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8304 (tp) REVERT: F 372 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8439 (p) REVERT: F 375 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6952 (tm) REVERT: G 175 GLU cc_start: 0.6973 (pt0) cc_final: 0.6611 (pt0) REVERT: G 204 LYS cc_start: 0.6668 (ttpt) cc_final: 0.6462 (tttp) REVERT: G 289 THR cc_start: 0.7667 (t) cc_final: 0.7160 (p) REVERT: G 423 ARG cc_start: 0.7126 (mtp-110) cc_final: 0.6447 (mtp-110) REVERT: G 424 GLU cc_start: 0.7249 (tt0) cc_final: 0.6569 (mm-30) REVERT: G 430 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.5750 (mp10) REVERT: H 182 ILE cc_start: 0.8189 (mt) cc_final: 0.7752 (mm) REVERT: H 186 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7525 (tm) REVERT: H 282 SER cc_start: 0.9142 (p) cc_final: 0.8810 (m) REVERT: H 332 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7462 (mtp85) REVERT: H 351 ASP cc_start: 0.7433 (t0) cc_final: 0.7045 (t0) REVERT: H 399 SER cc_start: 0.8415 (m) cc_final: 0.7959 (t) REVERT: H 413 MET cc_start: 0.8503 (mtp) cc_final: 0.8217 (mtp) REVERT: H 444 ARG cc_start: 0.7848 (mtm180) cc_final: 0.7611 (mtm180) REVERT: I 163 GLN cc_start: 0.8411 (pt0) cc_final: 0.8178 (pt0) REVERT: I 173 SER cc_start: 0.7759 (t) cc_final: 0.7518 (p) REVERT: I 253 SER cc_start: 0.9226 (m) cc_final: 0.8946 (m) REVERT: I 410 ASN cc_start: 0.9165 (t0) cc_final: 0.8697 (t0) REVERT: I 430 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: J 211 GLU cc_start: 0.8585 (tt0) cc_final: 0.8285 (tt0) REVERT: J 257 ASP cc_start: 0.7184 (m-30) cc_final: 0.6969 (m-30) REVERT: J 261 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: J 311 VAL cc_start: 0.8625 (t) cc_final: 0.8342 (p) REVERT: J 358 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7815 (mt-10) REVERT: J 375 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6359 (tm) REVERT: J 382 ILE cc_start: 0.8495 (mm) cc_final: 0.8249 (tt) REVERT: J 392 TYR cc_start: 0.7295 (m-80) cc_final: 0.6647 (m-80) REVERT: J 422 GLU cc_start: 0.6820 (tt0) cc_final: 0.6544 (tt0) REVERT: J 438 GLN cc_start: 0.8414 (tt0) cc_final: 0.8202 (tt0) REVERT: J 443 GLN cc_start: 0.7736 (tt0) cc_final: 0.7536 (tt0) REVERT: K 172 GLU cc_start: 0.0081 (OUTLIER) cc_final: -0.0570 (tt0) REVERT: K 186 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7022 (tm) REVERT: K 272 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.6747 (mmm160) REVERT: K 325 LYS cc_start: 0.8306 (ttpt) cc_final: 0.8082 (ttmt) REVERT: K 329 LYS cc_start: 0.7682 (mttt) cc_final: 0.7381 (mtpt) REVERT: K 358 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6461 (mp0) REVERT: K 399 SER cc_start: 0.7851 (m) cc_final: 0.7490 (m) REVERT: K 402 PHE cc_start: 0.7910 (p90) cc_final: 0.7706 (p90) REVERT: L 169 VAL cc_start: 0.6912 (OUTLIER) cc_final: 0.6688 (m) REVERT: L 175 GLU cc_start: 0.5162 (OUTLIER) cc_final: 0.1818 (tt0) REVERT: L 181 ARG cc_start: 0.5774 (ttp-170) cc_final: 0.5342 (ttp-170) REVERT: L 230 THR cc_start: 0.6792 (p) cc_final: 0.6553 (p) REVERT: L 273 LYS cc_start: 0.7409 (mtpt) cc_final: 0.6539 (mmtt) REVERT: L 375 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5821 (tm) REVERT: L 381 ARG cc_start: 0.8144 (mtp180) cc_final: 0.7919 (mmm160) REVERT: L 430 GLN cc_start: 0.1500 (OUTLIER) cc_final: 0.1140 (tt0) REVERT: a 38 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7382 (ptp-170) REVERT: a 60 TYR cc_start: 0.8168 (t80) cc_final: 0.7608 (t80) outliers start: 296 outliers final: 151 residues processed: 976 average time/residue: 0.3957 time to fit residues: 602.7763 Evaluate side-chains 747 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 571 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 362 TRP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 295 LYS Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 448 ASN Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 452 SER Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 203 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 270 LEU Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 295 LYS Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 349 SER Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 229 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 375 LEU Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain J residue 454 THR Chi-restraints excluded: chain K residue 172 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 203 SER Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 216 LYS Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 267 LEU Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 405 ILE Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain L residue 430 GLN Chi-restraints excluded: chain a residue 20 ILE Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 48 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 8 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 260 optimal weight: 8.9990 chunk 6 optimal weight: 0.2980 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 279 optimal weight: 6.9990 chunk 335 optimal weight: 8.9990 chunk 280 optimal weight: 10.0000 chunk 291 optimal weight: 9.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 GLN A 410 ASN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN C 363 GLN C 376 GLN D 363 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN ** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 HIS ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 ASN F 438 GLN F 448 ASN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 180 GLN ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 GLN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN I 398 ASN I 426 GLN ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 367 GLN L 438 GLN b 47 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.107455 restraints weight = 41498.735| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.01 r_work: 0.3026 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 29082 Z= 0.301 Angle : 0.745 8.370 39308 Z= 0.400 Chirality : 0.049 0.212 4568 Planarity : 0.005 0.051 5000 Dihedral : 9.297 80.239 4171 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.41 % Favored : 91.90 % Rotamer: Outliers : 8.33 % Allowed : 20.59 % Favored : 71.08 % 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: -1.57 (0.13), residues: 3656 helix: -0.60 (0.18), residues: 796 sheet: -0.80 (0.18), residues: 891 loop : -1.31 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 219 HIS 0.011 0.002 HIS A 279 PHE 0.021 0.002 PHE C 244 TYR 0.028 0.002 TYR E 392 ARG 0.008 0.001 ARG K 274 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 830) hydrogen bonds : angle 6.28672 ( 2268) covalent geometry : bond 0.00689 (29082) covalent geometry : angle 0.74479 (39308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 257 poor density : 573 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7412 (mmm-85) REVERT: A 363 GLN cc_start: 0.8279 (mt0) cc_final: 0.8067 (mt0) REVERT: A 378 GLN cc_start: 0.8258 (pm20) cc_final: 0.7765 (pp30) REVERT: A 413 MET cc_start: 0.9092 (mtp) cc_final: 0.8735 (mtm) REVERT: A 422 GLU cc_start: 0.7560 (tt0) cc_final: 0.7234 (tt0) REVERT: B 204 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7364 (mptt) REVERT: B 240 LYS cc_start: 0.8722 (mttt) cc_final: 0.8407 (mttt) REVERT: B 267 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7491 (tp) REVERT: B 289 THR cc_start: 0.8772 (p) cc_final: 0.8514 (p) REVERT: B 336 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7627 (ptt-90) REVERT: B 346 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8639 (tp) REVERT: C 279 HIS cc_start: 0.8890 (OUTLIER) cc_final: 0.8391 (m-70) REVERT: C 375 LEU cc_start: 0.9153 (mm) cc_final: 0.8901 (mt) REVERT: D 362 TRP cc_start: 0.9226 (OUTLIER) cc_final: 0.7811 (m-90) REVERT: E 372 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8486 (p) REVERT: F 181 ARG cc_start: 0.8087 (mtp180) cc_final: 0.7694 (mtp85) REVERT: F 182 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8666 (mm) REVERT: F 185 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7067 (t0) REVERT: F 233 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: F 346 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8546 (tp) REVERT: G 204 LYS cc_start: 0.7057 (ttpt) cc_final: 0.5850 (mmtm) REVERT: G 240 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7447 (tppt) REVERT: G 284 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7376 (tm-30) REVERT: G 305 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7287 (mt-10) REVERT: G 376 GLN cc_start: 0.6894 (mm-40) cc_final: 0.6680 (mm-40) REVERT: G 382 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8030 (pt) REVERT: G 430 GLN cc_start: 0.6130 (OUTLIER) cc_final: 0.4998 (mp10) REVERT: H 186 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7620 (tm) REVERT: H 198 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: H 285 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: H 332 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7805 (mtp85) REVERT: H 363 GLN cc_start: 0.8067 (mt0) cc_final: 0.7849 (mt0) REVERT: H 399 SER cc_start: 0.8497 (m) cc_final: 0.7965 (t) REVERT: H 444 ARG cc_start: 0.8148 (mtm180) cc_final: 0.7634 (mtm180) REVERT: I 208 MET cc_start: 0.8932 (mtp) cc_final: 0.8660 (mtm) REVERT: I 253 SER cc_start: 0.9296 (m) cc_final: 0.9045 (m) REVERT: I 410 ASN cc_start: 0.9396 (t0) cc_final: 0.8979 (t0) REVERT: I 430 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7395 (mp10) REVERT: I 437 THR cc_start: 0.8650 (p) cc_final: 0.8435 (p) REVERT: J 261 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8206 (mt-10) REVERT: J 311 VAL cc_start: 0.8802 (t) cc_final: 0.8524 (p) REVERT: J 358 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7497 (mt-10) REVERT: J 422 GLU cc_start: 0.7469 (tt0) cc_final: 0.7192 (tt0) REVERT: J 430 GLN cc_start: 0.6887 (mm-40) cc_final: 0.6512 (mm-40) REVERT: J 438 GLN cc_start: 0.8520 (tt0) cc_final: 0.8132 (tt0) REVERT: J 443 GLN cc_start: 0.8114 (tt0) cc_final: 0.7707 (tt0) REVERT: K 172 GLU cc_start: 0.0970 (OUTLIER) cc_final: -0.0093 (tt0) REVERT: K 186 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7175 (tm) REVERT: K 272 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7312 (ttm-80) REVERT: K 329 LYS cc_start: 0.7865 (mttt) cc_final: 0.7654 (mtpt) REVERT: K 358 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6624 (mp0) REVERT: K 359 ASP cc_start: 0.8356 (t0) cc_final: 0.8145 (t70) REVERT: K 425 ARG cc_start: 0.8146 (tpt170) cc_final: 0.7810 (tpt170) REVERT: L 175 GLU cc_start: 0.5377 (OUTLIER) cc_final: 0.2052 (tt0) REVERT: L 273 LYS cc_start: 0.7417 (mtpt) cc_final: 0.6437 (mmtt) REVERT: L 417 ARG cc_start: 0.6175 (mtp180) cc_final: 0.5910 (mtm-85) REVERT: L 444 ARG cc_start: 0.6587 (ttp-110) cc_final: 0.6157 (ttp-110) REVERT: a 60 TYR cc_start: 0.8296 (t80) cc_final: 0.7632 (t80) outliers start: 257 outliers final: 160 residues processed: 750 average time/residue: 0.4100 time to fit residues: 479.5626 Evaluate side-chains 696 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 513 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 362 TRP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 438 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 452 SER Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 203 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 279 HIS Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 295 LYS Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain J residue 454 THR Chi-restraints excluded: chain K residue 172 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 205 ILE Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 208 MET Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 276 ILE Chi-restraints excluded: chain K residue 283 ILE Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 219 TRP Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 48 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 284 optimal weight: 0.7980 chunk 264 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 303 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN C 376 GLN ** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 GLN G 180 GLN ** G 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN H 410 ASN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 GLN I 367 GLN I 398 ASN ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 376 GLN ** K 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 367 GLN ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 28 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.115856 restraints weight = 41008.616| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.04 r_work: 0.3131 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29082 Z= 0.131 Angle : 0.579 7.817 39308 Z= 0.313 Chirality : 0.043 0.204 4568 Planarity : 0.004 0.041 5000 Dihedral : 8.144 85.492 4133 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.84 % Favored : 92.56 % Rotamer: Outliers : 6.74 % Allowed : 22.54 % Favored : 70.72 % 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: -1.31 (0.14), residues: 3656 helix: -0.41 (0.18), residues: 786 sheet: -0.65 (0.18), residues: 892 loop : -1.12 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 219 HIS 0.008 0.001 HIS D 279 PHE 0.015 0.001 PHE L 254 TYR 0.018 0.001 TYR E 392 ARG 0.007 0.001 ARG H 184 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 830) hydrogen bonds : angle 5.83430 ( 2268) covalent geometry : bond 0.00286 (29082) covalent geometry : angle 0.57934 (39308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 604 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7560 (tt0) REVERT: A 289 THR cc_start: 0.8846 (p) cc_final: 0.8608 (p) REVERT: A 336 ARG cc_start: 0.8383 (mtm-85) cc_final: 0.8129 (mtm180) REVERT: A 363 GLN cc_start: 0.8303 (mt0) cc_final: 0.7935 (mt0) REVERT: A 378 GLN cc_start: 0.8060 (pm20) cc_final: 0.7659 (pp30) REVERT: A 413 MET cc_start: 0.8982 (mtp) cc_final: 0.8708 (mtm) REVERT: A 422 GLU cc_start: 0.7564 (tt0) cc_final: 0.7336 (tt0) REVERT: B 204 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7111 (mptt) REVERT: B 240 LYS cc_start: 0.8683 (mttt) cc_final: 0.8369 (mttt) REVERT: B 267 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7506 (tp) REVERT: B 289 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8274 (p) REVERT: C 236 LYS cc_start: 0.5661 (mmtt) cc_final: 0.5374 (mmtt) REVERT: C 241 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7664 (mt-10) REVERT: C 279 HIS cc_start: 0.8786 (OUTLIER) cc_final: 0.8383 (m-70) REVERT: C 375 LEU cc_start: 0.9008 (mm) cc_final: 0.8799 (mt) REVERT: D 258 GLU cc_start: 0.6392 (tt0) cc_final: 0.5871 (tt0) REVERT: D 288 MET cc_start: 0.9111 (mmm) cc_final: 0.8482 (mmt) REVERT: D 362 TRP cc_start: 0.9153 (OUTLIER) cc_final: 0.7888 (m-90) REVERT: D 378 GLN cc_start: 0.8186 (pt0) cc_final: 0.7918 (pt0) REVERT: E 239 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8760 (mt) REVERT: E 426 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.6857 (mp10) REVERT: F 163 GLN cc_start: 0.8461 (mt0) cc_final: 0.8257 (mt0) REVERT: F 181 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7731 (mtp85) REVERT: F 182 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8569 (mm) REVERT: F 185 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7010 (t0) REVERT: F 346 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8332 (tp) REVERT: F 378 GLN cc_start: 0.8253 (pm20) cc_final: 0.8028 (pm20) REVERT: F 426 GLN cc_start: 0.8433 (mt0) cc_final: 0.8079 (mt0) REVERT: G 204 LYS cc_start: 0.7053 (ttpt) cc_final: 0.5627 (mmtt) REVERT: G 240 LYS cc_start: 0.7813 (tttp) cc_final: 0.7402 (tppt) REVERT: G 287 PHE cc_start: 0.8278 (m-10) cc_final: 0.8002 (m-80) REVERT: G 297 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7125 (tttm) REVERT: G 305 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6969 (mm-30) REVERT: G 364 ASP cc_start: 0.8275 (m-30) cc_final: 0.7781 (m-30) REVERT: G 417 ARG cc_start: 0.7973 (ttm170) cc_final: 0.7680 (mtm110) REVERT: G 424 GLU cc_start: 0.7344 (tt0) cc_final: 0.6576 (mm-30) REVERT: G 430 GLN cc_start: 0.5957 (OUTLIER) cc_final: 0.4648 (mp10) REVERT: H 186 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7446 (tm) REVERT: H 285 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7602 (mt-10) REVERT: H 329 LYS cc_start: 0.8939 (mtpp) cc_final: 0.8672 (mtmm) REVERT: H 363 GLN cc_start: 0.8042 (mt0) cc_final: 0.7646 (mt0) REVERT: H 399 SER cc_start: 0.8400 (m) cc_final: 0.8048 (t) REVERT: H 444 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7578 (mtm180) REVERT: I 253 SER cc_start: 0.9268 (m) cc_final: 0.8974 (m) REVERT: I 410 ASN cc_start: 0.9240 (t0) cc_final: 0.8881 (t0) REVERT: I 430 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7500 (mp10) REVERT: J 311 VAL cc_start: 0.8671 (t) cc_final: 0.8380 (p) REVERT: J 358 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7398 (mt-10) REVERT: J 422 GLU cc_start: 0.7212 (tt0) cc_final: 0.6797 (tt0) REVERT: J 438 GLN cc_start: 0.8221 (tt0) cc_final: 0.8016 (tt0) REVERT: J 443 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: K 186 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7174 (tm) REVERT: K 274 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7736 (mmm-85) REVERT: K 329 LYS cc_start: 0.7673 (mttt) cc_final: 0.7469 (mtpt) REVERT: K 358 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6655 (mp0) REVERT: K 399 SER cc_start: 0.7621 (m) cc_final: 0.7244 (m) REVERT: K 417 ARG cc_start: 0.7522 (ttm170) cc_final: 0.7272 (ttm170) REVERT: K 419 VAL cc_start: 0.6303 (OUTLIER) cc_final: 0.6018 (t) REVERT: L 169 VAL cc_start: 0.6605 (OUTLIER) cc_final: 0.6350 (m) REVERT: L 175 GLU cc_start: 0.4459 (OUTLIER) cc_final: 0.1725 (tt0) REVERT: L 273 LYS cc_start: 0.7285 (mtpt) cc_final: 0.6467 (mmtt) REVERT: L 305 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7413 (mt-10) REVERT: L 330 LEU cc_start: 0.8561 (mt) cc_final: 0.8244 (mt) REVERT: L 351 ASP cc_start: 0.8366 (p0) cc_final: 0.7472 (t70) REVERT: L 417 ARG cc_start: 0.6126 (OUTLIER) cc_final: 0.5830 (mtm-85) REVERT: L 444 ARG cc_start: 0.6575 (ttp-110) cc_final: 0.6251 (ptm-80) REVERT: a 58 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: a 60 TYR cc_start: 0.8088 (t80) cc_final: 0.7463 (t80) REVERT: b 37 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6334 (tt) outliers start: 208 outliers final: 122 residues processed: 747 average time/residue: 0.4039 time to fit residues: 474.0571 Evaluate side-chains 662 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 518 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 362 TRP Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain J residue 443 GLN Chi-restraints excluded: chain J residue 454 THR Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 208 MET Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 276 ILE Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 259 THR Chi-restraints excluded: chain L residue 283 ILE Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 350 MET Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 417 ARG Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain L residue 436 VAL Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 48 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 311 optimal weight: 9.9990 chunk 265 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 295 optimal weight: 7.9990 chunk 316 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 264 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 HIS B 363 GLN B 443 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 376 GLN G 180 GLN ** G 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN H 243 HIS H 410 ASN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN L 367 GLN ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.107980 restraints weight = 40985.407| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.08 r_work: 0.3015 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 29082 Z= 0.261 Angle : 0.665 9.033 39308 Z= 0.353 Chirality : 0.046 0.186 4568 Planarity : 0.005 0.053 5000 Dihedral : 7.971 81.104 4100 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.41 % Favored : 92.10 % Rotamer: Outliers : 7.81 % Allowed : 21.85 % Favored : 70.33 % 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: -1.33 (0.14), residues: 3656 helix: -0.50 (0.18), residues: 768 sheet: -0.66 (0.18), residues: 887 loop : -1.10 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 362 HIS 0.011 0.002 HIS J 279 PHE 0.020 0.002 PHE F 244 TYR 0.021 0.002 TYR C 392 ARG 0.006 0.001 ARG J 181 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 830) hydrogen bonds : angle 5.94141 ( 2268) covalent geometry : bond 0.00610 (29082) covalent geometry : angle 0.66477 (39308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 516 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.8552 (tp) cc_final: 0.8221 (tp) REVERT: A 304 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8553 (p) REVERT: A 363 GLN cc_start: 0.8252 (mt0) cc_final: 0.7921 (mt0) REVERT: A 413 MET cc_start: 0.8969 (mtp) cc_final: 0.8712 (mtm) REVERT: A 422 GLU cc_start: 0.7714 (tt0) cc_final: 0.6974 (tt0) REVERT: B 204 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7156 (mptt) REVERT: B 240 LYS cc_start: 0.8683 (mttt) cc_final: 0.8415 (mttt) REVERT: B 267 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7751 (tp) REVERT: B 289 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8360 (p) REVERT: B 364 ASP cc_start: 0.6428 (OUTLIER) cc_final: 0.6137 (t70) REVERT: C 175 GLU cc_start: 0.6435 (mm-30) cc_final: 0.5612 (pt0) REVERT: C 277 GLU cc_start: 0.8542 (tt0) cc_final: 0.8308 (tt0) REVERT: C 279 HIS cc_start: 0.8831 (OUTLIER) cc_final: 0.8402 (m-70) REVERT: C 375 LEU cc_start: 0.9212 (mm) cc_final: 0.8996 (mt) REVERT: C 429 LYS cc_start: 0.5965 (tptp) cc_final: 0.5480 (tptt) REVERT: D 258 GLU cc_start: 0.6518 (tt0) cc_final: 0.5949 (tt0) REVERT: D 288 MET cc_start: 0.9100 (mmm) cc_final: 0.8796 (mmt) REVERT: D 362 TRP cc_start: 0.9256 (OUTLIER) cc_final: 0.7806 (m-90) REVERT: E 175 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8052 (mt-10) REVERT: E 426 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.6519 (mp10) REVERT: F 182 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8657 (mm) REVERT: F 185 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7265 (t0) REVERT: F 233 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: G 172 GLU cc_start: 0.4132 (OUTLIER) cc_final: 0.3197 (pt0) REVERT: G 183 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8815 (pt) REVERT: G 240 LYS cc_start: 0.7692 (tttp) cc_final: 0.7314 (tppt) REVERT: G 297 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7196 (tttm) REVERT: G 305 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7138 (mm-30) REVERT: G 364 ASP cc_start: 0.8418 (m-30) cc_final: 0.7952 (m-30) REVERT: G 371 ASP cc_start: 0.8216 (t0) cc_final: 0.7960 (t0) REVERT: G 382 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8102 (mm) REVERT: G 392 TYR cc_start: 0.7651 (m-80) cc_final: 0.7146 (m-80) REVERT: G 430 GLN cc_start: 0.5988 (OUTLIER) cc_final: 0.4678 (mp10) REVERT: H 180 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8386 (mt0) REVERT: H 186 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7529 (tm) REVERT: H 198 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: H 285 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: H 399 SER cc_start: 0.8453 (m) cc_final: 0.8013 (t) REVERT: H 417 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8158 (ttm170) REVERT: I 253 SER cc_start: 0.9372 (m) cc_final: 0.9097 (m) REVERT: I 367 GLN cc_start: 0.7912 (mt0) cc_final: 0.7688 (mt0) REVERT: I 430 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7668 (mp10) REVERT: J 167 VAL cc_start: 0.6852 (OUTLIER) cc_final: 0.6582 (m) REVERT: J 184 ARG cc_start: 0.7576 (ptm160) cc_final: 0.6732 (ttp-110) REVERT: J 311 VAL cc_start: 0.8801 (t) cc_final: 0.8526 (p) REVERT: J 358 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7432 (mt-10) REVERT: J 422 GLU cc_start: 0.7452 (tt0) cc_final: 0.7153 (tt0) REVERT: J 438 GLN cc_start: 0.8483 (tt0) cc_final: 0.8064 (tt0) REVERT: J 443 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: K 186 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7032 (tm) REVERT: K 358 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6881 (mp0) REVERT: K 417 ARG cc_start: 0.7694 (ttm170) cc_final: 0.7436 (ttm170) REVERT: K 425 ARG cc_start: 0.8125 (tpt170) cc_final: 0.7850 (tpt170) REVERT: L 175 GLU cc_start: 0.4879 (OUTLIER) cc_final: 0.2067 (tt0) REVERT: L 273 LYS cc_start: 0.7237 (mtpt) cc_final: 0.6399 (mmtt) REVERT: L 295 LYS cc_start: 0.7876 (mptt) cc_final: 0.7289 (ptpp) REVERT: L 330 LEU cc_start: 0.8655 (mt) cc_final: 0.8273 (mt) REVERT: L 351 ASP cc_start: 0.8275 (p0) cc_final: 0.7590 (t70) REVERT: L 417 ARG cc_start: 0.6348 (OUTLIER) cc_final: 0.5894 (mtm110) REVERT: L 430 GLN cc_start: 0.1666 (OUTLIER) cc_final: 0.1118 (tt0) REVERT: L 444 ARG cc_start: 0.6532 (ttp-110) cc_final: 0.6039 (ttm170) REVERT: a 58 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7537 (tt0) outliers start: 241 outliers final: 171 residues processed: 688 average time/residue: 0.4027 time to fit residues: 438.5243 Evaluate side-chains 673 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 473 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 362 TRP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 273 LYS Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 448 ASN Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 409 ASP Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 203 SER Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 279 HIS Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 417 ARG Chi-restraints excluded: chain H residue 429 LYS Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 285 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 347 ILE Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain J residue 443 GLN Chi-restraints excluded: chain J residue 454 THR Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 208 MET Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 350 MET Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 432 ASP Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 182 ILE Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 219 TRP Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 283 ILE Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 350 MET Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 417 ARG Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain L residue 430 GLN Chi-restraints excluded: chain L residue 436 VAL Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 48 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 32 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 chunk 331 optimal weight: 20.0000 chunk 180 optimal weight: 50.0000 chunk 199 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 247 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN B 443 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 376 GLN G 180 GLN G 363 GLN G 438 GLN G 443 GLN ** H 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 GLN H 410 ASN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 GLN ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.111480 restraints weight = 40815.369| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.12 r_work: 0.3077 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29082 Z= 0.142 Angle : 0.564 6.950 39308 Z= 0.301 Chirality : 0.043 0.177 4568 Planarity : 0.004 0.060 5000 Dihedral : 7.493 85.066 4093 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.25 % Favored : 92.45 % Rotamer: Outliers : 6.61 % Allowed : 23.51 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.21 (0.14), residues: 3656 helix: -0.35 (0.18), residues: 757 sheet: -0.60 (0.18), residues: 884 loop : -1.03 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 362 HIS 0.007 0.001 HIS J 279 PHE 0.012 0.001 PHE E 265 TYR 0.014 0.001 TYR E 392 ARG 0.007 0.001 ARG F 415 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 830) hydrogen bonds : angle 5.70380 ( 2268) covalent geometry : bond 0.00316 (29082) covalent geometry : angle 0.56392 (39308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 543 time to evaluate : 3.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7529 (mp0) REVERT: A 257 ASP cc_start: 0.8107 (m-30) cc_final: 0.7904 (m-30) REVERT: A 268 LEU cc_start: 0.8568 (tp) cc_final: 0.8232 (tp) REVERT: A 289 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8601 (p) REVERT: A 297 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8174 (mtpp) REVERT: A 305 GLU cc_start: 0.7804 (pt0) cc_final: 0.7573 (pt0) REVERT: A 336 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8083 (mtm180) REVERT: A 351 ASP cc_start: 0.7916 (t0) cc_final: 0.7581 (t0) REVERT: A 363 GLN cc_start: 0.8232 (mt0) cc_final: 0.7889 (mt0) REVERT: A 378 GLN cc_start: 0.8150 (pm20) cc_final: 0.7869 (pp30) REVERT: A 413 MET cc_start: 0.8871 (mtp) cc_final: 0.8659 (mtm) REVERT: A 422 GLU cc_start: 0.7689 (tt0) cc_final: 0.6970 (tt0) REVERT: B 204 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7091 (mptt) REVERT: B 240 LYS cc_start: 0.8694 (mttt) cc_final: 0.8406 (mttt) REVERT: B 267 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7722 (tp) REVERT: C 175 GLU cc_start: 0.5883 (mm-30) cc_final: 0.5229 (pt0) REVERT: C 236 LYS cc_start: 0.6041 (mmtt) cc_final: 0.5525 (mmtt) REVERT: C 279 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8367 (m-70) REVERT: C 429 LYS cc_start: 0.5534 (tptp) cc_final: 0.5051 (tptt) REVERT: D 176 THR cc_start: 0.9046 (m) cc_final: 0.8833 (m) REVERT: D 258 GLU cc_start: 0.5975 (tt0) cc_final: 0.5647 (tt0) REVERT: D 288 MET cc_start: 0.9083 (mmm) cc_final: 0.8638 (mmt) REVERT: D 311 VAL cc_start: 0.9095 (t) cc_final: 0.8747 (p) REVERT: D 362 TRP cc_start: 0.9167 (OUTLIER) cc_final: 0.7873 (m-90) REVERT: D 443 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8176 (mm-40) REVERT: E 175 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7961 (mt-10) REVERT: E 426 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.6459 (mp10) REVERT: F 177 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8502 (mt) REVERT: F 182 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8454 (mm) REVERT: F 185 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7217 (t0) REVERT: F 426 GLN cc_start: 0.8422 (mt0) cc_final: 0.8167 (mt0) REVERT: G 172 GLU cc_start: 0.3858 (OUTLIER) cc_final: 0.3050 (pt0) REVERT: G 224 THR cc_start: 0.6506 (OUTLIER) cc_final: 0.6241 (p) REVERT: G 240 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7318 (tppt) REVERT: G 297 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7160 (tttm) REVERT: G 305 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7179 (mm-30) REVERT: G 311 VAL cc_start: 0.7864 (t) cc_final: 0.7180 (p) REVERT: G 319 SER cc_start: 0.7669 (t) cc_final: 0.7437 (m) REVERT: G 417 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7704 (ttp-170) REVERT: G 430 GLN cc_start: 0.6051 (OUTLIER) cc_final: 0.4900 (mp10) REVERT: H 186 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7305 (tm) REVERT: H 234 GLU cc_start: 0.7273 (tt0) cc_final: 0.6748 (tt0) REVERT: H 236 LYS cc_start: 0.8239 (ptmt) cc_final: 0.6134 (mmmt) REVERT: H 363 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: H 399 SER cc_start: 0.8316 (m) cc_final: 0.7972 (t) REVERT: I 253 SER cc_start: 0.9314 (m) cc_final: 0.9024 (m) REVERT: I 410 ASN cc_start: 0.9281 (t0) cc_final: 0.8921 (t0) REVERT: I 430 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: J 167 VAL cc_start: 0.6777 (OUTLIER) cc_final: 0.6501 (m) REVERT: J 181 ARG cc_start: 0.8201 (ttp80) cc_final: 0.7943 (ttp80) REVERT: J 184 ARG cc_start: 0.7390 (ptm160) cc_final: 0.6550 (ttp-110) REVERT: J 311 VAL cc_start: 0.8747 (t) cc_final: 0.8459 (p) REVERT: J 358 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7432 (mt-10) REVERT: J 422 GLU cc_start: 0.7407 (tt0) cc_final: 0.7098 (tt0) REVERT: J 438 GLN cc_start: 0.8364 (tt0) cc_final: 0.7935 (tt0) REVERT: J 443 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: K 186 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7164 (tm) REVERT: K 279 HIS cc_start: 0.7464 (OUTLIER) cc_final: 0.6907 (t-90) REVERT: K 342 SER cc_start: 0.8383 (p) cc_final: 0.8101 (t) REVERT: K 358 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6638 (mp0) REVERT: K 359 ASP cc_start: 0.8319 (t70) cc_final: 0.7787 (t0) REVERT: K 425 ARG cc_start: 0.8098 (tpt170) cc_final: 0.7793 (tpt170) REVERT: L 175 GLU cc_start: 0.4911 (OUTLIER) cc_final: 0.2099 (tt0) REVERT: L 273 LYS cc_start: 0.7412 (mtpt) cc_final: 0.6554 (mmtt) REVERT: L 330 LEU cc_start: 0.8648 (mt) cc_final: 0.8292 (mt) REVERT: L 351 ASP cc_start: 0.8279 (p0) cc_final: 0.7589 (t70) REVERT: L 444 ARG cc_start: 0.6602 (ttp-110) cc_final: 0.6361 (ptm-80) REVERT: a 58 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7447 (tt0) outliers start: 204 outliers final: 146 residues processed: 684 average time/residue: 0.4091 time to fit residues: 436.7372 Evaluate side-chains 676 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 505 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 362 TRP Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 443 GLN Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 438 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 279 HIS Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 363 GLN Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 285 GLU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 378 GLN Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain J residue 277 GLU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 347 ILE Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain J residue 443 GLN Chi-restraints excluded: chain J residue 454 THR Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 279 HIS Chi-restraints excluded: chain K residue 350 MET Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 219 TRP Chi-restraints excluded: chain L residue 297 LYS Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 350 MET Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 20 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 10 optimal weight: 0.9980 chunk 283 optimal weight: 0.9980 chunk 311 optimal weight: 8.9990 chunk 268 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 chunk 276 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 319 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN C 416 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN E 416 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 376 GLN G 180 GLN G 416 GLN H 363 GLN H 410 ASN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 367 GLN ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.134868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.109563 restraints weight = 40967.901| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.03 r_work: 0.3051 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.6290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29082 Z= 0.189 Angle : 0.596 8.411 39308 Z= 0.316 Chirality : 0.044 0.214 4568 Planarity : 0.004 0.045 5000 Dihedral : 7.352 83.073 4086 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.22 % Favored : 92.51 % Rotamer: Outliers : 6.78 % Allowed : 23.83 % Favored : 69.39 % 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: -1.17 (0.14), residues: 3656 helix: -0.32 (0.18), residues: 761 sheet: -0.61 (0.17), residues: 884 loop : -0.99 (0.14), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 362 HIS 0.009 0.001 HIS L 279 PHE 0.015 0.002 PHE E 265 TYR 0.015 0.001 TYR J 392 ARG 0.008 0.001 ARG L 415 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 830) hydrogen bonds : angle 5.70739 ( 2268) covalent geometry : bond 0.00435 (29082) covalent geometry : angle 0.59551 (39308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 492 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7462 (mp0) REVERT: A 268 LEU cc_start: 0.8615 (tp) cc_final: 0.8291 (tp) REVERT: A 281 VAL cc_start: 0.8956 (t) cc_final: 0.8644 (m) REVERT: A 336 ARG cc_start: 0.8361 (mtm-85) cc_final: 0.8045 (mtm180) REVERT: A 351 ASP cc_start: 0.7955 (t0) cc_final: 0.7726 (t0) REVERT: A 363 GLN cc_start: 0.8217 (mt0) cc_final: 0.7909 (mt0) REVERT: A 378 GLN cc_start: 0.8166 (pm20) cc_final: 0.7877 (pp30) REVERT: A 413 MET cc_start: 0.8894 (mtp) cc_final: 0.8662 (mtm) REVERT: A 422 GLU cc_start: 0.8081 (tt0) cc_final: 0.7435 (tt0) REVERT: A 435 TYR cc_start: 0.8766 (m-80) cc_final: 0.8434 (m-80) REVERT: B 204 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.7043 (mptt) REVERT: B 240 LYS cc_start: 0.8658 (mttt) cc_final: 0.8404 (mttt) REVERT: B 264 ILE cc_start: 0.6957 (mp) cc_final: 0.6753 (mp) REVERT: B 267 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7766 (tp) REVERT: B 431 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7972 (ptp-170) REVERT: C 175 GLU cc_start: 0.6212 (mm-30) cc_final: 0.5181 (pt0) REVERT: C 279 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.8384 (m-70) REVERT: C 429 LYS cc_start: 0.5856 (tptp) cc_final: 0.5276 (tptt) REVERT: D 258 GLU cc_start: 0.6389 (tt0) cc_final: 0.5805 (tt0) REVERT: D 288 MET cc_start: 0.9037 (mmm) cc_final: 0.8699 (mmt) REVERT: D 362 TRP cc_start: 0.9219 (OUTLIER) cc_final: 0.7866 (m-90) REVERT: D 423 ARG cc_start: 0.7712 (ttt-90) cc_final: 0.7510 (ttt-90) REVERT: E 416 GLN cc_start: 0.7658 (tt0) cc_final: 0.7429 (tt0) REVERT: E 426 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.6527 (mp10) REVERT: F 185 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7248 (t0) REVERT: F 233 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: G 172 GLU cc_start: 0.3882 (OUTLIER) cc_final: 0.3070 (pt0) REVERT: G 224 THR cc_start: 0.6572 (OUTLIER) cc_final: 0.6317 (p) REVERT: G 240 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7367 (tppt) REVERT: G 297 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.6809 (tttm) REVERT: G 305 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7135 (mm-30) REVERT: G 319 SER cc_start: 0.7692 (t) cc_final: 0.7417 (m) REVERT: G 417 ARG cc_start: 0.8046 (ttm170) cc_final: 0.7647 (ttp-170) REVERT: G 430 GLN cc_start: 0.6047 (OUTLIER) cc_final: 0.4873 (mp10) REVERT: H 186 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7232 (tm) REVERT: H 236 LYS cc_start: 0.8180 (ptmt) cc_final: 0.6054 (mmmt) REVERT: H 363 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7717 (mt0) REVERT: H 399 SER cc_start: 0.8288 (m) cc_final: 0.7931 (t) REVERT: I 253 SER cc_start: 0.9385 (m) cc_final: 0.9095 (m) REVERT: I 410 ASN cc_start: 0.9304 (t0) cc_final: 0.8932 (t0) REVERT: I 416 GLN cc_start: 0.8475 (tt0) cc_final: 0.8191 (tt0) REVERT: I 430 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7708 (mp10) REVERT: J 167 VAL cc_start: 0.6788 (OUTLIER) cc_final: 0.6474 (m) REVERT: J 247 TYR cc_start: 0.7700 (m-10) cc_final: 0.7247 (m-80) REVERT: J 272 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.8021 (mmm-85) REVERT: J 311 VAL cc_start: 0.8786 (t) cc_final: 0.8517 (p) REVERT: J 358 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7397 (mt-10) REVERT: J 422 GLU cc_start: 0.7558 (tt0) cc_final: 0.7249 (tt0) REVERT: J 443 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: K 186 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7188 (tm) REVERT: K 190 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7181 (mt) REVERT: K 201 MET cc_start: 0.7942 (mtm) cc_final: 0.7495 (ptp) REVERT: K 279 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.7087 (t-90) REVERT: K 358 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6671 (mp0) REVERT: K 359 ASP cc_start: 0.8290 (t70) cc_final: 0.7782 (t0) REVERT: K 378 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: K 425 ARG cc_start: 0.8114 (tpt170) cc_final: 0.7806 (tpt170) REVERT: L 175 GLU cc_start: 0.5146 (OUTLIER) cc_final: 0.2216 (tt0) REVERT: L 273 LYS cc_start: 0.7392 (mtpt) cc_final: 0.6555 (mmtt) REVERT: L 330 LEU cc_start: 0.8644 (mt) cc_final: 0.8323 (mt) REVERT: L 351 ASP cc_start: 0.8245 (p0) cc_final: 0.7603 (t70) REVERT: L 430 GLN cc_start: 0.1781 (OUTLIER) cc_final: 0.1397 (tt0) REVERT: L 444 ARG cc_start: 0.6725 (ttp-110) cc_final: 0.5805 (ptm160) REVERT: a 58 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7443 (tt0) outliers start: 209 outliers final: 163 residues processed: 643 average time/residue: 0.3953 time to fit residues: 401.2604 Evaluate side-chains 661 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 473 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 362 TRP Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 443 GLN Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 438 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 448 ASN Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 304 SER Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 409 ASP Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 279 HIS Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 363 GLN Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 285 GLU Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 375 LEU Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 277 GLU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 347 ILE Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain J residue 419 VAL Chi-restraints excluded: chain J residue 443 GLN Chi-restraints excluded: chain J residue 454 THR Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 231 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 279 HIS Chi-restraints excluded: chain K residue 350 MET Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 378 GLN Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 219 TRP Chi-restraints excluded: chain L residue 283 ILE Chi-restraints excluded: chain L residue 297 LYS Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 350 MET Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain L residue 430 GLN Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain b residue 20 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 203 optimal weight: 0.9990 chunk 211 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 347 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 165 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN ** H 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 GLN H 410 ASN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 GLN ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 367 GLN ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.139060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.113810 restraints weight = 40811.856| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.15 r_work: 0.3104 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29082 Z= 0.124 Angle : 0.537 7.467 39308 Z= 0.286 Chirality : 0.042 0.170 4568 Planarity : 0.004 0.037 5000 Dihedral : 7.016 85.113 4086 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.11 % Favored : 92.67 % Rotamer: Outliers : 6.23 % Allowed : 24.71 % Favored : 69.07 % 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: -1.05 (0.14), residues: 3656 helix: -0.16 (0.18), residues: 761 sheet: -0.55 (0.18), residues: 858 loop : -0.92 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 362 HIS 0.007 0.001 HIS D 279 PHE 0.015 0.001 PHE G 244 TYR 0.013 0.001 TYR J 434 ARG 0.006 0.001 ARG F 272 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 830) hydrogen bonds : angle 5.53289 ( 2268) covalent geometry : bond 0.00273 (29082) covalent geometry : angle 0.53728 (39308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 539 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7369 (mp0) REVERT: A 249 LEU cc_start: 0.8880 (tp) cc_final: 0.8525 (tp) REVERT: A 254 PHE cc_start: 0.8068 (m-80) cc_final: 0.7740 (m-10) REVERT: A 268 LEU cc_start: 0.8626 (tp) cc_final: 0.8387 (tp) REVERT: A 285 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7153 (mt-10) REVERT: A 336 ARG cc_start: 0.8353 (mtm-85) cc_final: 0.8067 (mtm180) REVERT: A 363 GLN cc_start: 0.8237 (mt0) cc_final: 0.7937 (mt0) REVERT: A 378 GLN cc_start: 0.8160 (pm20) cc_final: 0.7873 (pp30) REVERT: A 422 GLU cc_start: 0.7759 (tt0) cc_final: 0.7168 (tt0) REVERT: A 438 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: B 175 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7608 (mt-10) REVERT: B 213 ASP cc_start: 0.7192 (m-30) cc_final: 0.6567 (t0) REVERT: B 240 LYS cc_start: 0.8635 (mttt) cc_final: 0.8384 (mttt) REVERT: B 267 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7671 (tp) REVERT: B 431 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8003 (ptp-170) REVERT: C 175 GLU cc_start: 0.6062 (mm-30) cc_final: 0.5084 (pt0) REVERT: C 279 HIS cc_start: 0.8717 (OUTLIER) cc_final: 0.8345 (m-70) REVERT: C 429 LYS cc_start: 0.5488 (tptp) cc_final: 0.5009 (tptt) REVERT: C 444 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8365 (ptt90) REVERT: D 188 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7867 (mtmt) REVERT: D 258 GLU cc_start: 0.5981 (tt0) cc_final: 0.5367 (tt0) REVERT: D 288 MET cc_start: 0.8975 (mmm) cc_final: 0.8522 (mmt) REVERT: D 311 VAL cc_start: 0.9089 (t) cc_final: 0.8758 (p) REVERT: E 426 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.6315 (mp10) REVERT: F 185 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7072 (t0) REVERT: G 172 GLU cc_start: 0.3795 (OUTLIER) cc_final: 0.3064 (pt0) REVERT: G 224 THR cc_start: 0.6408 (OUTLIER) cc_final: 0.6145 (p) REVERT: G 240 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7321 (tppt) REVERT: G 273 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7127 (mtmt) REVERT: G 297 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.6863 (tttm) REVERT: G 305 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7172 (mm-30) REVERT: G 319 SER cc_start: 0.7692 (t) cc_final: 0.7404 (m) REVERT: G 351 ASP cc_start: 0.8143 (t70) cc_final: 0.7004 (p0) REVERT: G 430 GLN cc_start: 0.6166 (OUTLIER) cc_final: 0.4861 (mp10) REVERT: H 186 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7097 (tm) REVERT: H 291 ASP cc_start: 0.8243 (p0) cc_final: 0.7641 (p0) REVERT: H 363 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7510 (mt0) REVERT: H 399 SER cc_start: 0.8168 (m) cc_final: 0.7750 (t) REVERT: I 253 SER cc_start: 0.9308 (m) cc_final: 0.9008 (m) REVERT: I 359 ASP cc_start: 0.8265 (t0) cc_final: 0.7889 (t0) REVERT: I 361 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7566 (mm-30) REVERT: I 410 ASN cc_start: 0.9264 (t0) cc_final: 0.8842 (t0) REVERT: I 416 GLN cc_start: 0.8213 (tt0) cc_final: 0.7899 (tt0) REVERT: I 430 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7533 (mp10) REVERT: I 448 ASN cc_start: 0.8420 (p0) cc_final: 0.8086 (p0) REVERT: J 167 VAL cc_start: 0.6852 (OUTLIER) cc_final: 0.6556 (m) REVERT: J 247 TYR cc_start: 0.7692 (m-10) cc_final: 0.7235 (m-80) REVERT: J 311 VAL cc_start: 0.8730 (t) cc_final: 0.8436 (p) REVERT: J 443 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: K 186 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7066 (tm) REVERT: K 201 MET cc_start: 0.7934 (mtm) cc_final: 0.7621 (ptp) REVERT: K 279 HIS cc_start: 0.7486 (OUTLIER) cc_final: 0.7138 (t-90) REVERT: K 358 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6602 (mp0) REVERT: K 359 ASP cc_start: 0.8235 (t70) cc_final: 0.7726 (t0) REVERT: K 378 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: K 417 ARG cc_start: 0.7542 (ttm170) cc_final: 0.7264 (ttt180) REVERT: K 425 ARG cc_start: 0.8076 (tpt170) cc_final: 0.7745 (tpt170) REVERT: L 175 GLU cc_start: 0.5116 (OUTLIER) cc_final: 0.2261 (tt0) REVERT: L 249 LEU cc_start: 0.7276 (tp) cc_final: 0.7006 (tp) REVERT: L 273 LYS cc_start: 0.7248 (mtpt) cc_final: 0.6490 (mmtt) REVERT: L 295 LYS cc_start: 0.7782 (mptt) cc_final: 0.7241 (ptpp) REVERT: L 330 LEU cc_start: 0.8616 (mt) cc_final: 0.8355 (mt) REVERT: L 351 ASP cc_start: 0.8147 (p0) cc_final: 0.7511 (t70) REVERT: L 444 ARG cc_start: 0.6756 (ttp-110) cc_final: 0.6514 (ttp80) REVERT: a 58 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7439 (tt0) outliers start: 192 outliers final: 130 residues processed: 674 average time/residue: 0.3915 time to fit residues: 418.0878 Evaluate side-chains 667 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 513 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 438 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 304 SER Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 363 GLN Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 375 LEU Chi-restraints excluded: chain I residue 378 GLN Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 277 GLU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain J residue 419 VAL Chi-restraints excluded: chain J residue 443 GLN Chi-restraints excluded: chain J residue 454 THR Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 279 HIS Chi-restraints excluded: chain K residue 378 GLN Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 219 TRP Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 350 MET Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain b residue 20 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 94 optimal weight: 0.0170 chunk 275 optimal weight: 0.7980 chunk 304 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 216 optimal weight: 7.9990 chunk 180 optimal weight: 0.0020 chunk 77 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 300 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.5630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN H 363 GLN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 367 GLN ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113606 restraints weight = 40869.362| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.09 r_work: 0.3093 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29082 Z= 0.141 Angle : 0.550 8.171 39308 Z= 0.292 Chirality : 0.043 0.187 4568 Planarity : 0.004 0.036 5000 Dihedral : 6.836 83.996 4076 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.28 % Favored : 92.51 % Rotamer: Outliers : 5.97 % Allowed : 25.52 % Favored : 68.51 % 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: -1.03 (0.14), residues: 3656 helix: -0.18 (0.18), residues: 766 sheet: -0.47 (0.18), residues: 852 loop : -0.93 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 362 HIS 0.007 0.001 HIS D 279 PHE 0.022 0.001 PHE G 244 TYR 0.015 0.001 TYR J 434 ARG 0.006 0.001 ARG F 272 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 830) hydrogen bonds : angle 5.52209 ( 2268) covalent geometry : bond 0.00320 (29082) covalent geometry : angle 0.55007 (39308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 524 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7402 (mp0) REVERT: A 249 LEU cc_start: 0.8890 (tp) cc_final: 0.8542 (tp) REVERT: A 268 LEU cc_start: 0.8637 (tp) cc_final: 0.8377 (tp) REVERT: A 297 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8218 (mtpp) REVERT: A 336 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.8054 (mtm180) REVERT: A 363 GLN cc_start: 0.8248 (mt0) cc_final: 0.7951 (mt0) REVERT: A 378 GLN cc_start: 0.8183 (pm20) cc_final: 0.7904 (pp30) REVERT: A 382 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8745 (pt) REVERT: A 422 GLU cc_start: 0.7999 (tt0) cc_final: 0.7404 (tt0) REVERT: B 175 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7704 (mt-10) REVERT: B 216 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7508 (tppt) REVERT: B 240 LYS cc_start: 0.8738 (mttt) cc_final: 0.8467 (mttt) REVERT: B 267 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8103 (tp) REVERT: B 431 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8066 (ptp-170) REVERT: C 175 GLU cc_start: 0.6065 (mm-30) cc_final: 0.5013 (pt0) REVERT: C 211 GLU cc_start: 0.8117 (tt0) cc_final: 0.7800 (tt0) REVERT: C 279 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.8326 (m-70) REVERT: C 429 LYS cc_start: 0.5498 (tptp) cc_final: 0.4889 (tptt) REVERT: C 444 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8346 (ptt90) REVERT: D 258 GLU cc_start: 0.6169 (tt0) cc_final: 0.5515 (tt0) REVERT: D 288 MET cc_start: 0.9000 (mmm) cc_final: 0.8632 (mmt) REVERT: D 311 VAL cc_start: 0.9127 (t) cc_final: 0.8794 (p) REVERT: E 350 MET cc_start: 0.8432 (tpp) cc_final: 0.7876 (tpp) REVERT: E 426 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.6482 (mp10) REVERT: F 185 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7061 (t0) REVERT: F 233 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: F 281 VAL cc_start: 0.8912 (t) cc_final: 0.8644 (t) REVERT: G 172 GLU cc_start: 0.3816 (OUTLIER) cc_final: 0.3063 (pt0) REVERT: G 189 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6859 (mm-30) REVERT: G 224 THR cc_start: 0.6542 (OUTLIER) cc_final: 0.6290 (p) REVERT: G 240 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7326 (tppt) REVERT: G 273 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7167 (mtmt) REVERT: G 285 GLU cc_start: 0.8038 (tt0) cc_final: 0.7796 (tt0) REVERT: G 297 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.6900 (tttm) REVERT: G 305 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7103 (mm-30) REVERT: G 319 SER cc_start: 0.7761 (t) cc_final: 0.7443 (m) REVERT: G 351 ASP cc_start: 0.8185 (t70) cc_final: 0.6933 (p0) REVERT: G 392 TYR cc_start: 0.7580 (m-80) cc_final: 0.7144 (m-80) REVERT: G 430 GLN cc_start: 0.6083 (OUTLIER) cc_final: 0.5012 (mp10) REVERT: H 186 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7098 (tm) REVERT: H 198 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: H 291 ASP cc_start: 0.8234 (p0) cc_final: 0.8015 (p0) REVERT: H 295 LYS cc_start: 0.7770 (mttp) cc_final: 0.7535 (mtmt) REVERT: H 399 SER cc_start: 0.8188 (m) cc_final: 0.7786 (t) REVERT: I 253 SER cc_start: 0.9311 (m) cc_final: 0.9010 (m) REVERT: I 359 ASP cc_start: 0.8266 (t0) cc_final: 0.7898 (t0) REVERT: I 361 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7552 (mm-30) REVERT: I 410 ASN cc_start: 0.9272 (t0) cc_final: 0.8948 (t0) REVERT: I 416 GLN cc_start: 0.8211 (tt0) cc_final: 0.7859 (tt0) REVERT: J 167 VAL cc_start: 0.6854 (OUTLIER) cc_final: 0.6538 (m) REVERT: J 211 GLU cc_start: 0.8604 (tt0) cc_final: 0.8279 (mt-10) REVERT: J 247 TYR cc_start: 0.7780 (m-10) cc_final: 0.7324 (m-80) REVERT: J 311 VAL cc_start: 0.8705 (t) cc_final: 0.8393 (p) REVERT: J 443 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: K 186 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7040 (tm) REVERT: K 201 MET cc_start: 0.7910 (mtm) cc_final: 0.7659 (ptp) REVERT: K 279 HIS cc_start: 0.7407 (OUTLIER) cc_final: 0.7205 (t-90) REVERT: K 358 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6767 (mp0) REVERT: K 359 ASP cc_start: 0.8238 (t70) cc_final: 0.7771 (t0) REVERT: K 417 ARG cc_start: 0.7555 (ttm170) cc_final: 0.7309 (ttt180) REVERT: K 425 ARG cc_start: 0.8075 (tpt170) cc_final: 0.7726 (tpt170) REVERT: L 175 GLU cc_start: 0.5121 (OUTLIER) cc_final: 0.2217 (tt0) REVERT: L 249 LEU cc_start: 0.7338 (tp) cc_final: 0.7002 (tp) REVERT: L 273 LYS cc_start: 0.7233 (mtpt) cc_final: 0.6486 (mmtt) REVERT: L 295 LYS cc_start: 0.7709 (mptt) cc_final: 0.7214 (ptpp) REVERT: L 330 LEU cc_start: 0.8633 (mt) cc_final: 0.8368 (mt) REVERT: L 351 ASP cc_start: 0.8085 (p0) cc_final: 0.7490 (t70) REVERT: L 444 ARG cc_start: 0.6493 (ttp-110) cc_final: 0.5972 (ttm170) REVERT: a 58 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7458 (tt0) outliers start: 184 outliers final: 137 residues processed: 654 average time/residue: 0.4189 time to fit residues: 434.0615 Evaluate side-chains 659 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 498 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 438 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 304 SER Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 409 ASP Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 285 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 375 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 277 GLU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain J residue 419 VAL Chi-restraints excluded: chain J residue 443 GLN Chi-restraints excluded: chain J residue 454 THR Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 279 HIS Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 219 TRP Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 350 MET Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain b residue 20 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 302 optimal weight: 8.9990 chunk 326 optimal weight: 7.9990 chunk 324 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 352 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 256 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 GLN A 438 GLN B 363 GLN B 443 GLN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 416 GLN H 367 GLN H 410 ASN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.105898 restraints weight = 41327.322| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.06 r_work: 0.2997 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.6498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 29082 Z= 0.289 Angle : 0.679 8.633 39308 Z= 0.356 Chirality : 0.047 0.217 4568 Planarity : 0.005 0.049 5000 Dihedral : 7.216 81.758 4072 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.10 % Favored : 91.68 % Rotamer: Outliers : 5.84 % Allowed : 25.94 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.31 (0.13), residues: 3656 helix: -0.48 (0.17), residues: 806 sheet: -0.56 (0.18), residues: 815 loop : -1.13 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 362 HIS 0.010 0.002 HIS D 279 PHE 0.022 0.002 PHE E 265 TYR 0.021 0.002 TYR J 434 ARG 0.008 0.001 ARG F 181 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 830) hydrogen bonds : angle 5.87765 ( 2268) covalent geometry : bond 0.00681 (29082) covalent geometry : angle 0.67869 (39308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 519 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7483 (mp0) REVERT: A 363 GLN cc_start: 0.8262 (mt0) cc_final: 0.7951 (mt0) REVERT: A 422 GLU cc_start: 0.7996 (tt0) cc_final: 0.7338 (tt0) REVERT: A 429 LYS cc_start: 0.8144 (mtmt) cc_final: 0.6905 (tptt) REVERT: B 240 LYS cc_start: 0.8694 (mttt) cc_final: 0.8397 (mttt) REVERT: B 267 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8071 (tp) REVERT: B 431 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8094 (ptp-170) REVERT: C 175 GLU cc_start: 0.6524 (mm-30) cc_final: 0.5025 (pt0) REVERT: C 211 GLU cc_start: 0.8201 (tt0) cc_final: 0.7929 (tt0) REVERT: C 258 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6390 (mt-10) REVERT: C 279 HIS cc_start: 0.8851 (OUTLIER) cc_final: 0.8416 (m-70) REVERT: C 284 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: C 429 LYS cc_start: 0.6038 (tptp) cc_final: 0.5420 (tptt) REVERT: D 258 GLU cc_start: 0.6848 (tt0) cc_final: 0.6337 (tt0) REVERT: D 288 MET cc_start: 0.8904 (mmm) cc_final: 0.8672 (mmt) REVERT: D 311 VAL cc_start: 0.9277 (t) cc_final: 0.8999 (p) REVERT: E 216 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8185 (mtpt) REVERT: E 426 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.6415 (mp10) REVERT: F 185 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7319 (t0) REVERT: F 233 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: G 172 GLU cc_start: 0.3843 (OUTLIER) cc_final: 0.3004 (pt0) REVERT: G 204 LYS cc_start: 0.7286 (ttpt) cc_final: 0.5667 (mmtt) REVERT: G 240 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7246 (tppt) REVERT: G 285 GLU cc_start: 0.8131 (tt0) cc_final: 0.7785 (tt0) REVERT: G 417 ARG cc_start: 0.8143 (ttm170) cc_final: 0.7872 (ttp-170) REVERT: G 430 GLN cc_start: 0.6122 (OUTLIER) cc_final: 0.4922 (mp10) REVERT: G 435 TYR cc_start: 0.6681 (m-80) cc_final: 0.5934 (m-80) REVERT: H 186 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7238 (tm) REVERT: H 198 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: H 291 ASP cc_start: 0.8219 (p0) cc_final: 0.7971 (p0) REVERT: H 295 LYS cc_start: 0.7994 (mttp) cc_final: 0.7656 (mtmt) REVERT: H 399 SER cc_start: 0.8283 (m) cc_final: 0.7882 (t) REVERT: I 208 MET cc_start: 0.9130 (ptp) cc_final: 0.8884 (ptm) REVERT: I 253 SER cc_start: 0.9338 (m) cc_final: 0.9037 (m) REVERT: I 315 LYS cc_start: 0.8317 (tptt) cc_final: 0.8027 (mmmt) REVERT: I 367 GLN cc_start: 0.7980 (mt0) cc_final: 0.7689 (mt0) REVERT: J 167 VAL cc_start: 0.6847 (OUTLIER) cc_final: 0.6558 (m) REVERT: J 247 TYR cc_start: 0.7822 (m-10) cc_final: 0.7447 (m-10) REVERT: J 272 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.8090 (mmm-85) REVERT: J 443 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8143 (mt0) REVERT: K 201 MET cc_start: 0.7806 (mtm) cc_final: 0.7542 (ptp) REVERT: K 279 HIS cc_start: 0.7300 (OUTLIER) cc_final: 0.6984 (t-90) REVERT: K 358 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6762 (mp0) REVERT: K 359 ASP cc_start: 0.8336 (t70) cc_final: 0.7879 (t0) REVERT: K 378 GLN cc_start: 0.8225 (pm20) cc_final: 0.7556 (pm20) REVERT: K 425 ARG cc_start: 0.7889 (tpt170) cc_final: 0.7527 (tpt170) REVERT: L 175 GLU cc_start: 0.5170 (OUTLIER) cc_final: 0.2234 (tt0) REVERT: L 249 LEU cc_start: 0.7426 (tp) cc_final: 0.6965 (tp) REVERT: L 273 LYS cc_start: 0.7281 (mtpt) cc_final: 0.6497 (mmtt) REVERT: L 295 LYS cc_start: 0.7746 (mptt) cc_final: 0.7236 (ptpp) REVERT: L 313 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7665 (pt0) REVERT: L 330 LEU cc_start: 0.8700 (mt) cc_final: 0.8446 (mt) REVERT: L 351 ASP cc_start: 0.8205 (p0) cc_final: 0.7612 (t70) REVERT: a 58 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: b 30 TYR cc_start: 0.7508 (m-10) cc_final: 0.7294 (m-10) outliers start: 180 outliers final: 145 residues processed: 647 average time/residue: 0.3930 time to fit residues: 402.9000 Evaluate side-chains 656 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 491 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 304 SER Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 409 ASP Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 270 LEU Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 279 HIS Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 285 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 375 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 277 GLU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain J residue 419 VAL Chi-restraints excluded: chain J residue 443 GLN Chi-restraints excluded: chain J residue 454 THR Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 279 HIS Chi-restraints excluded: chain K residue 350 MET Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 219 TRP Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 313 GLU Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 350 MET Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain b residue 20 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 172 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 255 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 354 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN B 443 GLN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 GLN H 410 ASN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 GLN I 367 GLN J 376 GLN K 279 HIS ** K 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 363 GLN L 367 GLN ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 49 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112731 restraints weight = 40714.579| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.03 r_work: 0.3124 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29082 Z= 0.120 Angle : 0.550 8.479 39308 Z= 0.292 Chirality : 0.043 0.217 4568 Planarity : 0.004 0.037 5000 Dihedral : 6.793 87.289 4069 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.14 % Favored : 92.67 % Rotamer: Outliers : 5.03 % Allowed : 26.82 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3656 helix: -0.36 (0.18), residues: 800 sheet: -0.53 (0.18), residues: 862 loop : -0.85 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 362 HIS 0.006 0.001 HIS H 279 PHE 0.012 0.001 PHE K 287 TYR 0.016 0.001 TYR A 225 ARG 0.008 0.001 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 830) hydrogen bonds : angle 5.56869 ( 2268) covalent geometry : bond 0.00261 (29082) covalent geometry : angle 0.54978 (39308) =============================================================================== Job complete usr+sys time: 17441.21 seconds wall clock time: 302 minutes 1.89 seconds (18121.89 seconds total)