Starting phenix.real_space_refine on Mon Aug 25 11:56:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zvi_60511/08_2025/8zvi_60511.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zvi_60511/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zvi_60511/08_2025/8zvi_60511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zvi_60511/08_2025/8zvi_60511.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zvi_60511/08_2025/8zvi_60511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zvi_60511/08_2025/8zvi_60511.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.85, per 1000 atoms: 0.20 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: 2.17 Conformation dependent library (CDL) restraints added in 905.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.99 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: 3.92 Time building geometry restraints manager: 2.77 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: 0.01 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: 2.960 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.790 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.860 ------------------------------------------------------------------------------- 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 : 24.03 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (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 ARG 0.012 0.002 ARG B 415 TYR 0.039 0.004 TYR J 445 PHE 0.033 0.004 PHE a 36 TRP 0.038 0.005 TRP I 219 HIS 0.015 0.003 HIS I 243 Details of bonding type rmsd covalent geometry : bond 0.02458 (29082) covalent geometry : angle 2.40379 (39308) hydrogen bonds : bond 0.25126 ( 830) hydrogen bonds : angle 9.26576 ( 2268) *********************** 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 : 1.093 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: 0.7004 (tptt) REVERT: A 295 LYS cc_start: 0.8832 (mttt) cc_final: 0.8616 (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: 0.8126 (tt) REVERT: A 363 GLN cc_start: 0.8547 (mt0) cc_final: 0.7901 (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: 0.6022 (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: 0.8700 (t) REVERT: B 205 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8336 (mt) REVERT: B 264 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.6365 (mp) REVERT: B 288 MET cc_start: 0.8652 (mmt) cc_final: 0.7608 (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: 0.8306 (mt) REVERT: B 430 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7614 (mt0) REVERT: B 446 PHE cc_start: 0.7491 (m-80) cc_final: 0.7269 (m-80) REVERT: C 165 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8557 (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: 0.7954 (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 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: 0.7343 (Cg_endo) REVERT: D 359 ASP cc_start: 0.7663 (t0) cc_final: 0.7371 (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: 0.8827 (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: 0.8514 (mm110) REVERT: F 168 GLU cc_start: 0.7258 (pt0) cc_final: 0.7044 (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: 0.8827 (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: 0.8847 (p) REVERT: F 346 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8851 (tp) REVERT: F 362 TRP cc_start: 0.8981 (OUTLIER) cc_final: 0.8311 (m-90) REVERT: F 372 SER cc_start: 0.7601 (OUTLIER) cc_final: 0.7358 (p) REVERT: F 382 ILE cc_start: 0.8957 (mm) cc_final: 0.8631 (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: 0.7720 (mt0) REVERT: F 450 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8675 (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: 0.8710 (mt) REVERT: G 255 ILE cc_start: 0.8403 (tt) cc_final: 0.8059 (tt) REVERT: G 312 THR cc_start: 0.7671 (p) cc_final: 0.7173 (t) REVERT: G 364 ASP cc_start: 0.7949 (m-30) cc_final: 0.7661 (m-30) REVERT: G 412 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8064 (m) REVERT: G 415 ARG cc_start: 0.7152 (ttm-80) cc_final: 0.6937 (ttm-80) REVERT: G 430 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.5272 (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: 0.7447 (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: 0.8182 (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: 0.8167 (p) REVERT: I 231 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8359 (p) REVERT: I 242 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8684 (pt) REVERT: I 252 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8329 (ptmt) REVERT: I 362 TRP cc_start: 0.8532 (OUTLIER) cc_final: 0.7392 (m-90) REVERT: I 398 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8743 (m-40) REVERT: I 410 ASN cc_start: 0.8605 (t0) cc_final: 0.8282 (t0) REVERT: J 213 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6698 (p0) REVERT: J 229 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8765 (p) REVERT: J 240 LYS cc_start: 0.8627 (mttt) cc_final: 0.8423 (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: 0.6989 (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: 0.6140 (tm) REVERT: K 270 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7445 (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: 0.7949 (p) REVERT: L 168 GLU cc_start: 0.5458 (mt-10) cc_final: 0.5216 (mt-10) REVERT: L 175 GLU cc_start: 0.5601 (OUTLIER) cc_final: 0.2458 (mt-10) REVERT: L 183 ILE cc_start: 0.5801 (OUTLIER) cc_final: 0.5376 (pt) REVERT: L 209 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5602 (mt) REVERT: L 236 LYS cc_start: 0.7202 (pttt) cc_final: 0.5933 (tppt) REVERT: L 273 LYS cc_start: 0.7468 (mtpt) cc_final: 0.7226 (mmtt) REVERT: L 372 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.7828 (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: 0.1745 time to fit residues: 410.2410 Evaluate side-chains 950 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 710 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** 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** F 448 ASN ** G 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.150310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.126185 restraints weight = 40842.815| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.14 r_work: 0.3259 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29082 Z= 0.194 Angle : 0.752 10.116 39308 Z= 0.412 Chirality : 0.048 0.331 4568 Planarity : 0.006 0.084 5000 Dihedral : 11.250 79.017 4422 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.18 % Favored : 93.05 % Rotamer: Outliers : 9.27 % Allowed : 19.58 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.13), residues: 3656 helix: -0.21 (0.18), residues: 789 sheet: -0.84 (0.18), residues: 871 loop : -1.36 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 444 TYR 0.028 0.002 TYR E 392 PHE 0.016 0.002 PHE G 178 TRP 0.014 0.002 TRP J 219 HIS 0.010 0.002 HIS D 279 Details of bonding type rmsd covalent geometry : bond 0.00427 (29082) covalent geometry : angle 0.75247 (39308) hydrogen bonds : bond 0.04915 ( 830) hydrogen bonds : angle 6.68312 ( 2268) *********************** 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 1103 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 286 poor density : 817 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7607 (mt-10) REVERT: A 175 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7823 (mt-10) REVERT: A 236 LYS cc_start: 0.7715 (pttt) cc_final: 0.6499 (tppt) REVERT: A 281 VAL cc_start: 0.9075 (t) cc_final: 0.8857 (t) REVERT: A 351 ASP cc_start: 0.7404 (t0) cc_final: 0.6937 (t0) REVERT: A 363 GLN cc_start: 0.8368 (mt0) cc_final: 0.8098 (mt0) REVERT: A 382 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8861 (pt) REVERT: A 410 ASN cc_start: 0.8808 (t0) cc_final: 0.8589 (t0) REVERT: A 413 MET cc_start: 0.9062 (mtp) cc_final: 0.8689 (mtm) REVERT: A 422 GLU cc_start: 0.6400 (tt0) cc_final: 0.6078 (tt0) REVERT: A 429 LYS cc_start: 0.7186 (mtmt) cc_final: 0.6697 (tptt) REVERT: A 435 TYR cc_start: 0.8380 (m-80) cc_final: 0.8100 (m-80) REVERT: B 181 ARG cc_start: 0.8133 (mtm110) cc_final: 0.7911 (mtp85) REVERT: B 186 LEU cc_start: 0.8002 (mt) cc_final: 0.7690 (mt) REVERT: B 204 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7319 (mptt) REVERT: B 240 LYS cc_start: 0.8607 (mttt) cc_final: 0.8262 (mttt) REVERT: B 267 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7575 (tp) REVERT: B 289 THR cc_start: 0.8724 (p) cc_final: 0.8454 (p) REVERT: B 376 GLN cc_start: 0.7129 (mt0) cc_final: 0.6843 (mt0) REVERT: B 413 MET cc_start: 0.8080 (mtp) cc_final: 0.7787 (mtp) REVERT: B 430 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7667 (mm-40) REVERT: C 264 ILE cc_start: 0.6680 (OUTLIER) cc_final: 0.6240 (mp) REVERT: D 197 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7656 (mt-10) REVERT: D 211 GLU cc_start: 0.8155 (tt0) cc_final: 0.7797 (mt-10) REVERT: D 288 MET cc_start: 0.9156 (mmm) cc_final: 0.8770 (mmt) REVERT: D 351 ASP cc_start: 0.7936 (t70) cc_final: 0.7460 (t0) REVERT: D 358 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7255 (mt-10) REVERT: D 362 TRP cc_start: 0.8985 (OUTLIER) cc_final: 0.7904 (m-90) REVERT: D 398 ASN cc_start: 0.7922 (m-40) cc_final: 0.7544 (m110) REVERT: D 421 VAL cc_start: 0.8259 (t) cc_final: 0.8033 (t) REVERT: E 167 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8267 (p) REVERT: E 197 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7360 (mm-30) REVERT: E 218 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.9034 (p) REVERT: E 362 TRP cc_start: 0.8895 (OUTLIER) cc_final: 0.8527 (m-90) REVERT: E 378 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7700 (pp30) REVERT: E 445 TYR cc_start: 0.8888 (m-10) cc_final: 0.8666 (m-80) REVERT: F 173 SER cc_start: 0.8552 (m) cc_final: 0.8349 (p) REVERT: F 185 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.6104 (t0) REVERT: F 234 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7701 (mt-10) REVERT: F 346 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8279 (tp) REVERT: F 372 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.7770 (p) REVERT: F 375 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6655 (tm) REVERT: F 376 GLN cc_start: 0.6044 (tt0) cc_final: 0.5832 (tt0) REVERT: F 417 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.7450 (ttp-170) REVERT: G 175 GLU cc_start: 0.7359 (pt0) cc_final: 0.6979 (pt0) REVERT: G 289 THR cc_start: 0.7657 (t) cc_final: 0.7175 (p) REVERT: G 382 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7916 (pt) REVERT: G 423 ARG cc_start: 0.6932 (mtp-110) cc_final: 0.6317 (mtp-110) REVERT: G 424 GLU cc_start: 0.7179 (tt0) cc_final: 0.6803 (mt-10) REVERT: G 430 GLN cc_start: 0.6903 (OUTLIER) cc_final: 0.5777 (mp10) REVERT: H 182 ILE cc_start: 0.8024 (mt) cc_final: 0.7620 (mm) REVERT: H 285 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7778 (tm-30) REVERT: H 332 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7508 (mtp85) REVERT: H 351 ASP cc_start: 0.7495 (t0) cc_final: 0.7032 (t0) REVERT: H 399 SER cc_start: 0.8330 (m) cc_final: 0.7894 (t) REVERT: I 173 SER cc_start: 0.7787 (t) cc_final: 0.7507 (p) REVERT: I 231 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8376 (p) REVERT: I 410 ASN cc_start: 0.8881 (t0) cc_final: 0.8413 (t0) REVERT: J 211 GLU cc_start: 0.8472 (tt0) cc_final: 0.8118 (tt0) REVERT: J 247 TYR cc_start: 0.7570 (m-10) cc_final: 0.7268 (m-10) REVERT: J 311 VAL cc_start: 0.8574 (t) cc_final: 0.8310 (p) REVERT: J 358 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7725 (mt-10) REVERT: J 375 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6056 (tm) REVERT: J 382 ILE cc_start: 0.8544 (mm) cc_final: 0.8224 (tt) REVERT: J 392 TYR cc_start: 0.7061 (m-80) cc_final: 0.6709 (m-80) REVERT: J 399 SER cc_start: 0.7671 (m) cc_final: 0.7359 (t) REVERT: K 172 GLU cc_start: -0.0022 (OUTLIER) cc_final: -0.0616 (tt0) REVERT: K 186 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6911 (tm) REVERT: K 272 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.6763 (mmm160) REVERT: K 329 LYS cc_start: 0.7434 (mttt) cc_final: 0.7146 (mtpt) REVERT: K 358 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6516 (mp0) REVERT: K 383 TYR cc_start: 0.8990 (m-80) cc_final: 0.8690 (m-80) REVERT: K 399 SER cc_start: 0.7782 (m) cc_final: 0.7437 (m) REVERT: L 169 VAL cc_start: 0.6891 (OUTLIER) cc_final: 0.6667 (m) REVERT: L 175 GLU cc_start: 0.5182 (OUTLIER) cc_final: 0.1724 (tt0) REVERT: L 188 LYS cc_start: 0.6575 (mttp) cc_final: 0.6141 (mttp) REVERT: L 273 LYS cc_start: 0.7440 (mtpt) cc_final: 0.6549 (mmtt) REVERT: L 375 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5564 (tm) REVERT: a 60 TYR cc_start: 0.8165 (t80) cc_final: 0.7563 (t80) outliers start: 286 outliers final: 152 residues processed: 1008 average time/residue: 0.1671 time to fit residues: 266.3997 Evaluate side-chains 772 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 597 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 227 THR Chi-restraints excluded: chain A residue 231 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 169 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 220 VAL 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 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 444 ARG Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 454 THR 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 264 ILE 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 365 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 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 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 E residue 167 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 362 TRP 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 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 192 VAL 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 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 378 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 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 382 ILE 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 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 295 LYS Chi-restraints excluded: chain H residue 349 SER Chi-restraints excluded: chain H residue 375 LEU 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 186 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain J residue 171 SER Chi-restraints excluded: chain J residue 176 THR 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 218 THR Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 284 GLU 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 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 a residue 20 ILE 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 48 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 138 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 301 optimal weight: 9.9990 chunk 198 optimal weight: 0.0010 chunk 350 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 327 optimal weight: 7.9990 chunk 358 optimal weight: 30.0000 chunk 245 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 293 optimal weight: 9.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- 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 367 GLN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN D 438 GLN ** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 ASN F 438 GLN G 243 HIS 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 367 GLN ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN ** K 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120930 restraints weight = 40688.211| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.11 r_work: 0.3201 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5014 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= 0.159 Angle : 0.624 8.173 39308 Z= 0.339 Chirality : 0.044 0.198 4568 Planarity : 0.004 0.043 5000 Dihedral : 8.666 89.532 4177 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.00 % Favored : 92.31 % Rotamer: Outliers : 7.46 % Allowed : 21.24 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.14), residues: 3656 helix: -0.35 (0.18), residues: 796 sheet: -0.68 (0.18), residues: 886 loop : -1.22 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 274 TYR 0.021 0.001 TYR A 225 PHE 0.016 0.001 PHE C 254 TRP 0.008 0.001 TRP L 219 HIS 0.007 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00344 (29082) covalent geometry : angle 0.62442 (39308) hydrogen bonds : bond 0.03963 ( 830) hydrogen bonds : angle 6.08755 ( 2268) *********************** 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 908 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 678 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.6703 (ttt90) REVERT: A 236 LYS cc_start: 0.7705 (pttt) cc_final: 0.6408 (tppt) REVERT: A 289 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8357 (p) REVERT: A 304 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8380 (p) REVERT: A 363 GLN cc_start: 0.8258 (mt0) cc_final: 0.8009 (mt0) REVERT: A 378 GLN cc_start: 0.7905 (pm20) cc_final: 0.7567 (pp30) REVERT: A 410 ASN cc_start: 0.8788 (t0) cc_final: 0.8587 (t0) REVERT: A 413 MET cc_start: 0.9012 (mtp) cc_final: 0.8634 (mtm) REVERT: A 422 GLU cc_start: 0.6757 (tt0) cc_final: 0.6461 (tt0) REVERT: A 426 GLN cc_start: 0.8178 (mt0) cc_final: 0.7809 (mt0) REVERT: A 429 LYS cc_start: 0.7423 (mtmt) cc_final: 0.6726 (tptt) REVERT: A 435 TYR cc_start: 0.8575 (m-80) cc_final: 0.8117 (m-80) REVERT: B 175 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7658 (mt-10) REVERT: B 186 LEU cc_start: 0.8396 (mt) cc_final: 0.8046 (mt) REVERT: B 204 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7371 (mptt) REVERT: B 240 LYS cc_start: 0.8700 (mttt) cc_final: 0.8328 (mttt) REVERT: B 267 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7502 (tp) REVERT: B 289 THR cc_start: 0.8653 (p) cc_final: 0.8371 (p) REVERT: B 350 MET cc_start: 0.8256 (ttt) cc_final: 0.7933 (ttt) REVERT: B 376 GLN cc_start: 0.7126 (mt0) cc_final: 0.6766 (mt0) REVERT: B 410 ASN cc_start: 0.8479 (t0) cc_final: 0.8240 (t0) REVERT: B 430 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.6717 (mp10) REVERT: B 444 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7068 (ptp-110) REVERT: C 211 GLU cc_start: 0.8152 (tt0) cc_final: 0.7613 (tt0) REVERT: C 277 GLU cc_start: 0.8512 (tt0) cc_final: 0.8243 (tt0) REVERT: C 279 HIS cc_start: 0.8748 (OUTLIER) cc_final: 0.8280 (m-70) REVERT: C 375 LEU cc_start: 0.8624 (mm) cc_final: 0.8229 (mp) REVERT: D 288 MET cc_start: 0.8966 (mmm) cc_final: 0.8702 (mmt) REVERT: D 351 ASP cc_start: 0.8125 (t70) cc_final: 0.7895 (t0) REVERT: D 362 TRP cc_start: 0.9013 (OUTLIER) cc_final: 0.7904 (m-90) REVERT: D 391 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7714 (mt-10) REVERT: D 398 ASN cc_start: 0.7936 (m-40) cc_final: 0.7683 (m-40) REVERT: E 167 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.7964 (p) REVERT: E 197 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7379 (mm-30) REVERT: E 239 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8773 (mt) REVERT: F 182 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8461 (mm) REVERT: F 185 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6356 (t0) REVERT: F 346 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8269 (tp) REVERT: F 371 ASP cc_start: 0.6985 (m-30) cc_final: 0.6617 (m-30) REVERT: F 424 GLU cc_start: 0.8274 (tt0) cc_final: 0.7950 (tt0) REVERT: F 426 GLN cc_start: 0.8352 (mt0) cc_final: 0.8001 (mt0) REVERT: G 240 LYS cc_start: 0.7813 (tttp) cc_final: 0.7441 (tppt) REVERT: G 392 TYR cc_start: 0.7137 (m-80) cc_final: 0.6933 (m-80) REVERT: G 417 ARG cc_start: 0.8021 (ttm170) cc_final: 0.7428 (mtm110) REVERT: G 424 GLU cc_start: 0.7435 (tt0) cc_final: 0.6635 (mm-30) REVERT: G 430 GLN cc_start: 0.6209 (OUTLIER) cc_final: 0.5064 (mp10) REVERT: H 285 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7563 (mt-10) REVERT: H 336 ARG cc_start: 0.8350 (ptp-170) cc_final: 0.7942 (ptp-170) REVERT: H 363 GLN cc_start: 0.7998 (mt0) cc_final: 0.7781 (mt0) REVERT: H 367 GLN cc_start: 0.7981 (tt0) cc_final: 0.7656 (tt0) REVERT: H 399 SER cc_start: 0.8310 (m) cc_final: 0.7958 (t) REVERT: H 444 ARG cc_start: 0.7772 (mtm180) cc_final: 0.7485 (mtm180) REVERT: I 173 SER cc_start: 0.7531 (t) cc_final: 0.7293 (p) REVERT: I 208 MET cc_start: 0.8843 (mtp) cc_final: 0.8539 (mtm) REVERT: I 359 ASP cc_start: 0.8193 (t0) cc_final: 0.7893 (t0) REVERT: I 410 ASN cc_start: 0.9204 (t0) cc_final: 0.8811 (t0) REVERT: J 211 GLU cc_start: 0.8362 (tt0) cc_final: 0.8134 (tt0) REVERT: J 261 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: J 311 VAL cc_start: 0.8553 (t) cc_final: 0.8283 (p) REVERT: J 358 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7550 (mt-10) REVERT: J 392 TYR cc_start: 0.7350 (m-80) cc_final: 0.6731 (m-80) REVERT: K 172 GLU cc_start: 0.0761 (OUTLIER) cc_final: -0.0238 (tt0) REVERT: K 181 ARG cc_start: 0.6324 (mtp180) cc_final: 0.6055 (mtp180) REVERT: K 186 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7110 (tm) REVERT: K 272 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7692 (ttt90) REVERT: K 300 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7302 (mp) REVERT: K 329 LYS cc_start: 0.7614 (mttt) cc_final: 0.7327 (mtpt) REVERT: K 358 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6733 (mp0) REVERT: K 399 SER cc_start: 0.7616 (m) cc_final: 0.7337 (m) REVERT: L 175 GLU cc_start: 0.5206 (OUTLIER) cc_final: 0.1996 (tt0) REVERT: L 189 GLU cc_start: 0.6620 (mm-30) cc_final: 0.6071 (mm-30) REVERT: L 216 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6921 (mmtm) REVERT: L 273 LYS cc_start: 0.7248 (mtpt) cc_final: 0.6408 (mmtt) REVERT: L 375 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5884 (tm) REVERT: L 430 GLN cc_start: 0.1159 (OUTLIER) cc_final: 0.0719 (tt0) REVERT: L 444 ARG cc_start: 0.6506 (ttp-110) cc_final: 0.5980 (ptm160) REVERT: L 450 VAL cc_start: 0.7397 (OUTLIER) cc_final: 0.7148 (t) REVERT: a 58 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: a 60 TYR cc_start: 0.8198 (t80) cc_final: 0.7492 (t80) outliers start: 230 outliers final: 130 residues processed: 836 average time/residue: 0.1657 time to fit residues: 218.7485 Evaluate side-chains 718 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 562 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 227 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 282 SER 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 368 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 191 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 204 LYS 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 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 444 ARG Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 206 LEU 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 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 379 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 169 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 218 THR 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 E residue 167 VAL Chi-restraints excluded: chain E residue 176 THR 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 311 VAL Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 368 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 169 VAL Chi-restraints excluded: chain F residue 171 SER 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 282 SER Chi-restraints excluded: chain F residue 283 ILE 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 166 SER Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 254 PHE 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 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 203 SER Chi-restraints excluded: chain H residue 205 ILE 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 283 ILE Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 419 VAL 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 375 LEU Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 207 THR 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 391 GLU Chi-restraints excluded: chain J residue 454 THR Chi-restraints excluded: chain K residue 172 GLU 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 218 THR 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 300 LEU 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 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 216 LYS 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 L residue 419 VAL Chi-restraints excluded: chain L residue 430 GLN Chi-restraints excluded: chain L residue 450 VAL Chi-restraints excluded: chain a residue 20 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 25 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 298 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 272 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 chunk 344 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 278 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN C 337 HIS ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 HIS ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 GLN F 378 GLN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN H 243 HIS H 410 ASN H 416 GLN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 GLN I 426 GLN ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 367 GLN ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.105886 restraints weight = 41217.816| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.18 r_work: 0.3004 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 29082 Z= 0.305 Angle : 0.735 7.830 39308 Z= 0.391 Chirality : 0.049 0.230 4568 Planarity : 0.005 0.049 5000 Dihedral : 8.266 79.155 4114 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.17 % Favored : 92.23 % Rotamer: Outliers : 8.14 % Allowed : 20.91 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.13), residues: 3656 helix: -0.67 (0.18), residues: 787 sheet: -0.65 (0.18), residues: 885 loop : -1.22 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 332 TYR 0.022 0.002 TYR A 225 PHE 0.026 0.003 PHE F 244 TRP 0.012 0.002 TRP L 219 HIS 0.009 0.002 HIS J 279 Details of bonding type rmsd covalent geometry : bond 0.00712 (29082) covalent geometry : angle 0.73534 (39308) hydrogen bonds : bond 0.04303 ( 830) hydrogen bonds : angle 6.14511 ( 2268) *********************** 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 805 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 251 poor density : 554 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8111 (mttt) REVERT: A 304 SER cc_start: 0.8896 (OUTLIER) cc_final: 0.8613 (p) REVERT: A 363 GLN cc_start: 0.8266 (mt0) cc_final: 0.7939 (mt0) REVERT: A 375 LEU cc_start: 0.9147 (mm) cc_final: 0.8901 (mt) REVERT: A 413 MET cc_start: 0.9079 (mtp) cc_final: 0.8772 (mtm) REVERT: A 422 GLU cc_start: 0.7541 (tt0) cc_final: 0.7291 (tt0) REVERT: B 204 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7178 (mptt) REVERT: B 240 LYS cc_start: 0.8665 (mttt) cc_final: 0.8315 (mttt) REVERT: B 289 THR cc_start: 0.8781 (p) cc_final: 0.8503 (p) REVERT: B 364 ASP cc_start: 0.6535 (OUTLIER) cc_final: 0.6329 (t70) REVERT: B 444 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7000 (ptp-110) REVERT: C 175 GLU cc_start: 0.6015 (mm-30) cc_final: 0.4948 (pt0) REVERT: C 277 GLU cc_start: 0.8611 (tt0) cc_final: 0.8365 (tt0) REVERT: C 279 HIS cc_start: 0.8891 (OUTLIER) cc_final: 0.8451 (m-70) REVERT: D 288 MET cc_start: 0.9105 (mmm) cc_final: 0.8793 (mmt) REVERT: D 362 TRP cc_start: 0.9286 (OUTLIER) cc_final: 0.7817 (m-90) REVERT: D 391 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8094 (mt-10) REVERT: E 175 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8066 (mt-10) REVERT: E 197 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7532 (mm-30) REVERT: E 363 GLN cc_start: 0.7963 (pp30) cc_final: 0.7721 (pp30) REVERT: E 448 ASN cc_start: 0.9375 (OUTLIER) cc_final: 0.9058 (p0) REVERT: F 182 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8630 (mm) REVERT: F 185 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7267 (t0) REVERT: F 233 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8054 (mt-10) REVERT: F 311 VAL cc_start: 0.9133 (t) cc_final: 0.8832 (m) REVERT: F 346 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8626 (tp) REVERT: G 205 ILE cc_start: 0.7593 (mt) cc_final: 0.7171 (mm) REVERT: G 240 LYS cc_start: 0.7807 (tttp) cc_final: 0.7340 (tppt) REVERT: G 364 ASP cc_start: 0.8193 (m-30) cc_final: 0.7799 (m-30) REVERT: G 371 ASP cc_start: 0.7967 (t0) cc_final: 0.7697 (t0) REVERT: G 382 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8149 (mm) REVERT: G 392 TYR cc_start: 0.7663 (m-80) cc_final: 0.7161 (m-80) REVERT: G 417 ARG cc_start: 0.8330 (ttm170) cc_final: 0.8087 (ttm170) REVERT: G 430 GLN cc_start: 0.6017 (OUTLIER) cc_final: 0.4781 (mp10) REVERT: H 186 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7546 (tm) REVERT: H 240 LYS cc_start: 0.8775 (mttt) cc_final: 0.8572 (mttt) REVERT: H 285 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7806 (mt-10) REVERT: H 329 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8681 (mtmm) REVERT: H 351 ASP cc_start: 0.7253 (t70) cc_final: 0.7038 (t70) REVERT: H 364 ASP cc_start: 0.8122 (m-30) cc_final: 0.7522 (m-30) REVERT: H 367 GLN cc_start: 0.8117 (tt0) cc_final: 0.7901 (mt0) REVERT: H 399 SER cc_start: 0.8406 (m) cc_final: 0.7853 (t) REVERT: H 444 ARG cc_start: 0.8028 (mtm180) cc_final: 0.7409 (mtm180) REVERT: I 208 MET cc_start: 0.8947 (mtp) cc_final: 0.8648 (mtm) REVERT: I 253 SER cc_start: 0.9371 (m) cc_final: 0.9085 (m) REVERT: I 289 THR cc_start: 0.8111 (p) cc_final: 0.7850 (p) REVERT: J 183 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8861 (pt) REVERT: J 311 VAL cc_start: 0.8783 (t) cc_final: 0.8427 (p) REVERT: J 358 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7523 (mt-10) REVERT: K 181 ARG cc_start: 0.6554 (mtp180) cc_final: 0.6322 (mtp180) REVERT: K 186 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7262 (tm) REVERT: K 199 LEU cc_start: 0.8136 (mp) cc_final: 0.7926 (mt) REVERT: K 329 LYS cc_start: 0.7708 (mttt) cc_final: 0.7488 (mtpt) REVERT: K 358 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6696 (mp0) REVERT: K 425 ARG cc_start: 0.8106 (tpt170) cc_final: 0.7855 (tpt170) REVERT: L 169 VAL cc_start: 0.6650 (OUTLIER) cc_final: 0.6426 (m) REVERT: L 175 GLU cc_start: 0.4880 (OUTLIER) cc_final: 0.1734 (tt0) REVERT: L 189 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6346 (mm-30) REVERT: L 273 LYS cc_start: 0.7179 (mtpt) cc_final: 0.6371 (mmtt) REVERT: L 295 LYS cc_start: 0.7813 (mptt) cc_final: 0.7234 (ptpp) REVERT: L 351 ASP cc_start: 0.8217 (p0) cc_final: 0.7291 (t70) REVERT: L 430 GLN cc_start: 0.1400 (OUTLIER) cc_final: 0.0869 (tt0) REVERT: L 444 ARG cc_start: 0.6430 (ttp-110) cc_final: 0.6157 (ttp80) outliers start: 251 outliers final: 161 residues processed: 729 average time/residue: 0.1589 time to fit residues: 185.6253 Evaluate side-chains 673 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 493 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL 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 304 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 399 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 176 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 409 ASP 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 444 ARG Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 MET 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 368 VAL 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 218 THR 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 283 ILE 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 368 VAL 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 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 378 GLN Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 448 ASN 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 233 GLU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 378 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 166 SER 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 253 SER Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain G residue 266 SER 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 320 VAL Chi-restraints excluded: chain G residue 321 LEU 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 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 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 182 ILE 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 205 ILE 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 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 454 THR Chi-restraints excluded: chain I residue 163 GLN 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 256 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain I residue 323 THR 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 J residue 176 THR Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 257 ASP 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 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 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 293 SER 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 432 ASP 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 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 312 THR 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 L residue 430 GLN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 6 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 334 optimal weight: 20.0000 chunk 23 optimal weight: 0.5980 chunk 331 optimal weight: 30.0000 chunk 170 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 245 optimal weight: 0.0770 chunk 308 optimal weight: 0.9980 chunk 203 optimal weight: 8.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN E 426 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 GLN G 180 GLN G 438 GLN G 443 GLN ** H 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 GLN H 376 GLN H 410 ASN H 416 GLN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 GLN I 180 GLN I 426 GLN ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 GLN ** K 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 441 ASN ** 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** a 28 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.140283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.112709 restraints weight = 40665.194| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.17 r_work: 0.3121 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29082 Z= 0.119 Angle : 0.571 7.559 39308 Z= 0.306 Chirality : 0.043 0.182 4568 Planarity : 0.004 0.043 5000 Dihedral : 7.417 86.549 4098 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.89 % Favored : 92.64 % Rotamer: Outliers : 5.93 % Allowed : 23.61 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.14), residues: 3656 helix: -0.56 (0.18), residues: 768 sheet: -0.56 (0.18), residues: 885 loop : -1.04 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 272 TYR 0.013 0.001 TYR J 392 PHE 0.013 0.001 PHE C 254 TRP 0.009 0.001 TRP L 219 HIS 0.010 0.001 HIS J 279 Details of bonding type rmsd covalent geometry : bond 0.00252 (29082) covalent geometry : angle 0.57128 (39308) hydrogen bonds : bond 0.03373 ( 830) hydrogen bonds : angle 5.76949 ( 2268) *********************** 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 755 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 572 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.8371 (mtmt) cc_final: 0.8123 (mttt) REVERT: A 285 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7855 (mt-10) REVERT: A 289 THR cc_start: 0.8751 (p) cc_final: 0.8515 (p) REVERT: A 363 GLN cc_start: 0.8228 (mt0) cc_final: 0.7835 (mt0) REVERT: A 367 GLN cc_start: 0.8654 (mt0) cc_final: 0.8292 (mt0) REVERT: A 378 GLN cc_start: 0.8135 (pm20) cc_final: 0.7866 (pp30) REVERT: A 382 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8743 (pt) REVERT: A 413 MET cc_start: 0.8915 (mtp) cc_final: 0.8679 (mtm) REVERT: A 422 GLU cc_start: 0.7625 (tt0) cc_final: 0.7232 (tt0) REVERT: A 429 LYS cc_start: 0.7921 (mtmt) cc_final: 0.6756 (tptt) REVERT: B 204 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7342 (mptt) REVERT: B 240 LYS cc_start: 0.8621 (mttt) cc_final: 0.8270 (mttt) REVERT: B 350 MET cc_start: 0.7777 (ttt) cc_final: 0.7526 (ttt) REVERT: B 364 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.6569 (t70) REVERT: C 175 GLU cc_start: 0.5554 (mm-30) cc_final: 0.4932 (pt0) REVERT: C 211 GLU cc_start: 0.8089 (tt0) cc_final: 0.7684 (tt0) REVERT: C 236 LYS cc_start: 0.5961 (mmtt) cc_final: 0.5594 (mmtt) REVERT: C 279 HIS cc_start: 0.8772 (OUTLIER) cc_final: 0.8348 (m-70) REVERT: D 258 GLU cc_start: 0.6013 (tt0) cc_final: 0.5300 (tt0) REVERT: D 288 MET cc_start: 0.9070 (mmm) cc_final: 0.8573 (mmt) REVERT: D 362 TRP cc_start: 0.9148 (OUTLIER) cc_final: 0.7921 (m-90) REVERT: D 391 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: D 443 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8646 (mm-40) REVERT: E 197 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7498 (mm-30) REVERT: E 239 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8705 (mt) REVERT: E 426 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.6809 (mp10) REVERT: F 182 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8427 (mm) REVERT: F 185 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7166 (t0) REVERT: F 346 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8475 (tp) REVERT: F 426 GLN cc_start: 0.8280 (mt0) cc_final: 0.8026 (mt0) REVERT: G 172 GLU cc_start: 0.4164 (OUTLIER) cc_final: 0.3169 (pt0) REVERT: G 205 ILE cc_start: 0.7519 (mt) cc_final: 0.7138 (mm) REVERT: G 240 LYS cc_start: 0.7784 (tttp) cc_final: 0.7367 (tppt) REVERT: G 305 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6725 (mm-30) REVERT: G 311 VAL cc_start: 0.7779 (t) cc_final: 0.7066 (p) REVERT: G 363 GLN cc_start: 0.8484 (mt0) cc_final: 0.8252 (mm-40) REVERT: G 392 TYR cc_start: 0.7205 (m-80) cc_final: 0.6675 (m-80) REVERT: G 430 GLN cc_start: 0.6338 (OUTLIER) cc_final: 0.5097 (mp10) REVERT: H 186 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7369 (tm) REVERT: H 198 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: H 270 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8633 (tp) REVERT: H 285 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7774 (mt-10) REVERT: H 306 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: H 329 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8669 (mtmm) REVERT: H 364 ASP cc_start: 0.8058 (m-30) cc_final: 0.7478 (m-30) REVERT: H 399 SER cc_start: 0.8224 (m) cc_final: 0.7866 (t) REVERT: I 253 SER cc_start: 0.9273 (m) cc_final: 0.8955 (m) REVERT: J 167 VAL cc_start: 0.6730 (OUTLIER) cc_final: 0.6474 (m) REVERT: J 183 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8753 (pt) REVERT: J 247 TYR cc_start: 0.7710 (m-10) cc_final: 0.7329 (m-10) REVERT: J 311 VAL cc_start: 0.8561 (t) cc_final: 0.8298 (p) REVERT: K 186 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7187 (tm) REVERT: K 199 LEU cc_start: 0.8029 (mp) cc_final: 0.7800 (mt) REVERT: K 329 LYS cc_start: 0.7609 (mttt) cc_final: 0.7294 (mtpt) REVERT: K 358 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6544 (mp0) REVERT: K 359 ASP cc_start: 0.8243 (t0) cc_final: 0.7832 (t70) REVERT: K 417 ARG cc_start: 0.7561 (ttm170) cc_final: 0.7300 (ttm170) REVERT: L 169 VAL cc_start: 0.6497 (OUTLIER) cc_final: 0.6243 (m) REVERT: L 175 GLU cc_start: 0.5022 (OUTLIER) cc_final: 0.2162 (tt0) REVERT: L 189 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6539 (mm-30) REVERT: L 273 LYS cc_start: 0.7345 (mtpt) cc_final: 0.6469 (mmtt) REVERT: L 295 LYS cc_start: 0.7769 (mptt) cc_final: 0.7152 (ptpp) REVERT: L 330 LEU cc_start: 0.8548 (mt) cc_final: 0.8164 (mt) REVERT: L 351 ASP cc_start: 0.8161 (p0) cc_final: 0.7331 (t70) REVERT: L 444 ARG cc_start: 0.6563 (ttp-110) cc_final: 0.6324 (ptm-80) REVERT: a 58 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: a 60 TYR cc_start: 0.8006 (t80) cc_final: 0.7382 (t80) outliers start: 183 outliers final: 113 residues processed: 704 average time/residue: 0.1632 time to fit residues: 183.4846 Evaluate side-chains 629 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 492 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL 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 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 191 VAL Chi-restraints excluded: chain B residue 195 LEU 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 227 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 409 ASP 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 454 THR Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 424 GLU 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 191 VAL Chi-restraints excluded: chain D residue 218 THR 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 310 VAL 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 D residue 391 GLU 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 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 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 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 177 ILE Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 348 VAL 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 440 VAL Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN 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 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 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 311 VAL Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 426 GLN Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 207 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 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU 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 205 ILE 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 276 ILE Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 182 ILE 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.345 > 50: distance: 109 - 115: 9.854 distance: 115 - 116: 8.674 distance: 116 - 117: 4.102 distance: 116 - 119: 7.890 distance: 117 - 118: 9.769 distance: 117 - 123: 4.021 distance: 119 - 120: 4.535 distance: 120 - 121: 9.764 distance: 120 - 122: 14.430 distance: 123 - 124: 4.174 distance: 124 - 125: 4.882 distance: 124 - 127: 4.126 distance: 125 - 134: 4.991 distance: 128 - 130: 3.089 distance: 129 - 131: 3.411 distance: 130 - 132: 5.843 distance: 131 - 133: 3.325 distance: 132 - 133: 8.520 distance: 134 - 135: 5.530 distance: 135 - 136: 8.873 distance: 135 - 138: 7.797 distance: 136 - 137: 6.343 distance: 136 - 141: 5.601 distance: 137 - 253: 3.233 distance: 138 - 139: 3.722 distance: 138 - 140: 3.675 distance: 141 - 142: 3.755 distance: 142 - 143: 8.898 distance: 142 - 145: 11.303 distance: 143 - 144: 9.239 distance: 143 - 149: 4.974 distance: 145 - 146: 13.637 distance: 146 - 147: 8.331 distance: 147 - 148: 8.264 distance: 149 - 150: 9.434 distance: 149 - 155: 10.747 distance: 150 - 151: 4.063 distance: 150 - 153: 10.552 distance: 151 - 152: 12.858 distance: 153 - 154: 11.822 distance: 154 - 155: 14.549 distance: 157 - 160: 3.286 distance: 158 - 159: 5.459 distance: 158 - 167: 6.286 distance: 160 - 161: 9.475 distance: 161 - 162: 5.880 distance: 162 - 163: 16.087 distance: 163 - 164: 11.074 distance: 164 - 165: 18.988 distance: 164 - 166: 14.035 distance: 167 - 168: 3.875 distance: 168 - 169: 6.654 distance: 168 - 171: 6.640 distance: 169 - 170: 4.857 distance: 169 - 176: 4.835 distance: 171 - 172: 3.001 distance: 172 - 173: 5.209 distance: 173 - 174: 4.681 distance: 173 - 175: 4.959 distance: 176 - 177: 12.330 distance: 177 - 178: 16.455 distance: 177 - 180: 9.919 distance: 178 - 179: 28.570 distance: 178 - 187: 10.631 distance: 180 - 181: 10.138 distance: 181 - 182: 8.771 distance: 182 - 183: 8.619 distance: 183 - 184: 6.278 distance: 184 - 185: 3.400 distance: 184 - 186: 9.515 distance: 187 - 188: 31.284 distance: 188 - 189: 26.250 distance: 188 - 191: 26.930 distance: 189 - 190: 7.698 distance: 189 - 192: 30.768 distance: 192 - 193: 11.292 distance: 193 - 194: 6.261 distance: 193 - 196: 5.932 distance: 194 - 195: 16.579 distance: 194 - 199: 13.034 distance: 196 - 197: 17.517 distance: 196 - 198: 6.734