Starting phenix.real_space_refine on Tue Jan 14 06:50:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xaw_38205/01_2025/8xaw_38205.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xaw_38205/01_2025/8xaw_38205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xaw_38205/01_2025/8xaw_38205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xaw_38205/01_2025/8xaw_38205.map" model { file = "/net/cci-nas-00/data/ceres_data/8xaw_38205/01_2025/8xaw_38205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xaw_38205/01_2025/8xaw_38205.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.071 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: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 6 5.21 5 S 84 5.16 5 C 31186 2.51 5 N 8170 2.21 5 O 9496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 48983 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4539 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 545} Chain: "B" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4539 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 545} Chain: "C" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4539 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 545} Chain: "D" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4513 Classifications: {'peptide': 563} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 541} Chain breaks: 1 Chain: "E" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4539 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 545} Chain: "F" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4539 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 545} Chain: "G" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "H" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "I" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "J" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "K" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "L" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "M" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "N" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "O" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "P" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "Q" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1426 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 162} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "S" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 266 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "T" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.29, per 1000 atoms: 0.41 Number of scatterers: 48983 At special positions: 0 Unit cell: (186.2, 186.2, 200.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 41 15.00 Mg 6 11.99 O 9496 8.00 N 8170 7.00 C 31186 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.44 Conformation dependent library (CDL) restraints added in 4.7 seconds 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11322 Finding SS restraints... Secondary structure from input PDB file: 253 helices and 28 sheets defined 43.8% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 30 through 35 removed outlier: 3.524A pdb=" N GLU A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.806A pdb=" N TYR A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.519A pdb=" N PHE A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.841A pdb=" N LEU A 214 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.508A pdb=" N GLU A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 249 removed outlier: 3.526A pdb=" N LEU A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 269 through 281 Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.925A pdb=" N PHE A 311 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.666A pdb=" N ASP A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 357 through 367 removed outlier: 3.525A pdb=" N LEU A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 414 removed outlier: 4.249A pdb=" N SER A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ILE A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.760A pdb=" N TYR A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 440 through 458 removed outlier: 5.486A pdb=" N ARG A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LYS A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.681A pdb=" N GLU A 470 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 489 through 500 Processing helix chain 'A' and resid 509 through 514 removed outlier: 3.785A pdb=" N SER A 513 " --> pdb=" O ASN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 554 Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'B' and resid 28 through 35 removed outlier: 4.358A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 114 removed outlier: 3.700A pdb=" N TYR B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.692A pdb=" N LYS B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 170 Processing helix chain 'B' and resid 211 through 215 removed outlier: 3.564A pdb=" N LEU B 215 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.917A pdb=" N PHE B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 249 removed outlier: 3.909A pdb=" N VAL B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 238 " --> pdb=" O GLN B 234 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 281 removed outlier: 3.519A pdb=" N VAL B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 removed outlier: 3.908A pdb=" N LYS B 312 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.625A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 351 through 354 Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 384 through 414 removed outlier: 3.784A pdb=" N LYS B 408 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 440 through 453 removed outlier: 3.566A pdb=" N ALA B 446 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 504 through 511 removed outlier: 3.638A pdb=" N ILE B 507 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 510 " --> pdb=" O ILE B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 571 removed outlier: 3.702A pdb=" N GLN B 567 " --> pdb=" O LYS B 563 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 104 through 114 removed outlier: 4.105A pdb=" N TYR C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 145 removed outlier: 3.550A pdb=" N PHE C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 170 Processing helix chain 'C' and resid 192 through 197 removed outlier: 4.104A pdb=" N ALA C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.577A pdb=" N LEU C 215 " --> pdb=" O TYR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.589A pdb=" N GLU C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 249 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 269 through 281 Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.703A pdb=" N PHE C 311 " --> pdb=" O HIS C 308 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS C 312 " --> pdb=" O ARG C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 342 Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.663A pdb=" N SER C 355 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 366 Processing helix chain 'C' and resid 384 through 411 removed outlier: 4.187A pdb=" N ILE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 431 Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 440 through 454 Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 467 through 471 removed outlier: 3.718A pdb=" N GLU C 470 " --> pdb=" O ARG C 467 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 471 " --> pdb=" O PRO C 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 467 through 471' Processing helix chain 'C' and resid 472 through 479 removed outlier: 4.149A pdb=" N GLN C 478 " --> pdb=" O THR C 474 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS C 479 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 499 removed outlier: 3.519A pdb=" N LEU C 499 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 505 Processing helix chain 'C' and resid 506 through 511 removed outlier: 3.683A pdb=" N ASN C 509 " --> pdb=" O ASP C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 554 removed outlier: 3.924A pdb=" N LYS C 554 " --> pdb=" O ASP C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 571 removed outlier: 3.600A pdb=" N ILE C 564 " --> pdb=" O GLU C 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 35 removed outlier: 4.242A pdb=" N ALA D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 114 removed outlier: 4.143A pdb=" N TYR D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.581A pdb=" N LYS D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 Processing helix chain 'D' and resid 211 through 215 Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.649A pdb=" N GLU D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 249 Processing helix chain 'D' and resid 255 through 260 removed outlier: 4.153A pdb=" N ILE D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 282 Processing helix chain 'D' and resid 306 through 311 removed outlier: 3.686A pdb=" N PHE D 311 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 341 removed outlier: 3.588A pdb=" N SER D 338 " --> pdb=" O ASP D 334 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 344 No H-bonds generated for 'chain 'D' and resid 342 through 344' Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 351 through 354 Processing helix chain 'D' and resid 357 through 366 Processing helix chain 'D' and resid 384 through 413 removed outlier: 3.815A pdb=" N ILE D 390 " --> pdb=" O GLU D 386 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 454 removed outlier: 3.514A pdb=" N LYS D 444 " --> pdb=" O TYR D 440 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU D 445 " --> pdb=" O ARG D 441 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA D 446 " --> pdb=" O THR D 442 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 447 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 471 removed outlier: 3.686A pdb=" N GLU D 470 " --> pdb=" O ARG D 467 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 471 " --> pdb=" O PRO D 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 467 through 471' Processing helix chain 'D' and resid 472 through 477 Processing helix chain 'D' and resid 489 through 500 removed outlier: 3.558A pdb=" N LEU D 500 " --> pdb=" O VAL D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 511 Processing helix chain 'D' and resid 547 through 553 Processing helix chain 'D' and resid 561 through 571 removed outlier: 3.847A pdb=" N GLN D 567 " --> pdb=" O LYS D 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 35 removed outlier: 4.259A pdb=" N ALA E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.842A pdb=" N TYR E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 145 removed outlier: 3.698A pdb=" N LYS E 145 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 171 Processing helix chain 'E' and resid 192 through 197 removed outlier: 3.969A pdb=" N ALA E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 215 removed outlier: 3.542A pdb=" N LEU E 214 " --> pdb=" O PRO E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 Processing helix chain 'E' and resid 231 through 249 removed outlier: 3.552A pdb=" N LEU E 244 " --> pdb=" O GLN E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 259 removed outlier: 3.859A pdb=" N ILE E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 Processing helix chain 'E' and resid 306 through 312 removed outlier: 3.731A pdb=" N LYS E 312 " --> pdb=" O ARG E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 341 removed outlier: 3.639A pdb=" N ARG E 335 " --> pdb=" O ASN E 331 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE E 340 " --> pdb=" O LEU E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 351 through 354 Processing helix chain 'E' and resid 357 through 366 Processing helix chain 'E' and resid 387 through 413 removed outlier: 3.526A pdb=" N PHE E 402 " --> pdb=" O LEU E 398 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS E 412 " --> pdb=" O LYS E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 432 removed outlier: 4.313A pdb=" N TYR E 431 " --> pdb=" O GLU E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 439 No H-bonds generated for 'chain 'E' and resid 437 through 439' Processing helix chain 'E' and resid 440 through 453 removed outlier: 3.625A pdb=" N ILE E 450 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 457 Processing helix chain 'E' and resid 467 through 471 Processing helix chain 'E' and resid 472 through 477 Processing helix chain 'E' and resid 489 through 499 Processing helix chain 'E' and resid 547 through 554 removed outlier: 3.515A pdb=" N LYS E 554 " --> pdb=" O ASP E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 571 removed outlier: 4.681A pdb=" N ASP E 562 " --> pdb=" O ASP E 558 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS E 563 " --> pdb=" O SER E 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 36 removed outlier: 4.295A pdb=" N ALA F 32 " --> pdb=" O GLU F 28 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU F 36 " --> pdb=" O ALA F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 114 removed outlier: 3.799A pdb=" N TYR F 112 " --> pdb=" O ILE F 108 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.908A pdb=" N PHE F 143 " --> pdb=" O GLY F 139 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN F 144 " --> pdb=" O ASN F 140 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS F 145 " --> pdb=" O ARG F 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 139 through 145' Processing helix chain 'F' and resid 156 through 168 Processing helix chain 'F' and resid 211 through 215 removed outlier: 3.545A pdb=" N LEU F 214 " --> pdb=" O PRO F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 225 removed outlier: 3.610A pdb=" N GLU F 222 " --> pdb=" O ASP F 218 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 250 removed outlier: 3.750A pdb=" N ARG F 235 " --> pdb=" O ASP F 231 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN F 236 " --> pdb=" O HIS F 232 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL F 237 " --> pdb=" O ASN F 233 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE F 238 " --> pdb=" O GLN F 234 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG F 239 " --> pdb=" O ARG F 235 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU F 244 " --> pdb=" O GLN F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 257 Processing helix chain 'F' and resid 269 through 281 Processing helix chain 'F' and resid 305 through 312 removed outlier: 3.687A pdb=" N HIS F 308 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE F 311 " --> pdb=" O HIS F 308 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS F 312 " --> pdb=" O ARG F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 341 Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 356 removed outlier: 3.885A pdb=" N LYS F 354 " --> pdb=" O GLY F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 366 removed outlier: 3.681A pdb=" N THR F 361 " --> pdb=" O THR F 357 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU F 362 " --> pdb=" O PHE F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 405 removed outlier: 4.528A pdb=" N SER F 389 " --> pdb=" O PHE F 385 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ILE F 390 " --> pdb=" O GLU F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 413 removed outlier: 4.132A pdb=" N ILE F 409 " --> pdb=" O HIS F 405 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS F 410 " --> pdb=" O SER F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 432 removed outlier: 3.963A pdb=" N TYR F 431 " --> pdb=" O GLU F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 454 Processing helix chain 'F' and resid 467 through 471 Processing helix chain 'F' and resid 472 through 477 Processing helix chain 'F' and resid 489 through 500 removed outlier: 3.517A pdb=" N LEU F 499 " --> pdb=" O TYR F 495 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 511 Processing helix chain 'F' and resid 547 through 553 Processing helix chain 'F' and resid 558 through 571 removed outlier: 4.516A pdb=" N ASP F 562 " --> pdb=" O ASP F 558 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS F 563 " --> pdb=" O SER F 559 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE F 565 " --> pdb=" O PHE F 561 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN F 567 " --> pdb=" O LYS F 563 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 169 removed outlier: 3.855A pdb=" N LYS G 158 " --> pdb=" O ASP G 154 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE G 164 " --> pdb=" O THR G 160 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN G 166 " --> pdb=" O GLN G 162 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE G 168 " --> pdb=" O ILE G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 178 removed outlier: 4.074A pdb=" N HIS G 177 " --> pdb=" O TYR G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 192 removed outlier: 3.528A pdb=" N ARG G 185 " --> pdb=" O SER G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 209 removed outlier: 3.633A pdb=" N VAL G 205 " --> pdb=" O LYS G 201 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU G 206 " --> pdb=" O SER G 202 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER G 207 " --> pdb=" O ASP G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 224 Processing helix chain 'G' and resid 224 through 237 removed outlier: 3.656A pdb=" N LEU G 229 " --> pdb=" O ARG G 225 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG G 230 " --> pdb=" O LYS G 226 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU G 234 " --> pdb=" O ARG G 230 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE G 236 " --> pdb=" O LEU G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 274 removed outlier: 4.198A pdb=" N CYS G 266 " --> pdb=" O THR G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 309 removed outlier: 3.643A pdb=" N GLU G 309 " --> pdb=" O GLN G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 335 removed outlier: 4.187A pdb=" N LEU G 329 " --> pdb=" O THR G 325 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER G 334 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 355 removed outlier: 3.579A pdb=" N SER G 355 " --> pdb=" O GLU G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 394 removed outlier: 4.224A pdb=" N LYS G 391 " --> pdb=" O PHE G 387 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU G 392 " --> pdb=" O ALA G 388 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE G 393 " --> pdb=" O ASP G 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 155 No H-bonds generated for 'chain 'H' and resid 153 through 155' Processing helix chain 'H' and resid 156 through 169 removed outlier: 3.910A pdb=" N ILE H 161 " --> pdb=" O LYS H 157 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLN H 162 " --> pdb=" O LYS H 158 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE H 164 " --> pdb=" O THR H 160 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS H 167 " --> pdb=" O ILE H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 177 Processing helix chain 'H' and resid 179 through 192 removed outlier: 3.948A pdb=" N ARG H 185 " --> pdb=" O SER H 181 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS H 186 " --> pdb=" O ASN H 182 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE H 190 " --> pdb=" O LYS H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 208 Processing helix chain 'H' and resid 224 through 234 removed outlier: 3.709A pdb=" N LEU H 229 " --> pdb=" O ARG H 225 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG H 230 " --> pdb=" O LYS H 226 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU H 234 " --> pdb=" O ARG H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 274 removed outlier: 3.568A pdb=" N CYS H 266 " --> pdb=" O THR H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 309 removed outlier: 3.520A pdb=" N LEU H 302 " --> pdb=" O ASN H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 334 removed outlier: 4.270A pdb=" N LEU H 329 " --> pdb=" O THR H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 355 removed outlier: 3.933A pdb=" N GLU H 351 " --> pdb=" O ASP H 347 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR H 352 " --> pdb=" O ASP H 348 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN H 354 " --> pdb=" O ASN H 350 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER H 355 " --> pdb=" O GLU H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 394 removed outlier: 4.206A pdb=" N GLU H 392 " --> pdb=" O ALA H 388 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE H 393 " --> pdb=" O ASP H 389 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 169 Processing helix chain 'I' and resid 172 through 178 removed outlier: 3.586A pdb=" N GLU I 176 " --> pdb=" O ASP I 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS I 177 " --> pdb=" O TYR I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 190 removed outlier: 3.682A pdb=" N ASN I 182 " --> pdb=" O TYR I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 209 Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'I' and resid 224 through 234 Processing helix chain 'I' and resid 259 through 274 removed outlier: 3.606A pdb=" N VAL I 263 " --> pdb=" O ASP I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 309 removed outlier: 3.619A pdb=" N GLU I 309 " --> pdb=" O GLN I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 334 removed outlier: 3.625A pdb=" N ILE I 330 " --> pdb=" O PRO I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.800A pdb=" N GLU I 351 " --> pdb=" O ASP I 347 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN I 354 " --> pdb=" O ASN I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 386 through 390 Processing helix chain 'J' and resid 159 through 169 removed outlier: 3.915A pdb=" N ILE J 163 " --> pdb=" O GLU J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 177 removed outlier: 3.599A pdb=" N GLU J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS J 177 " --> pdb=" O TYR J 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 172 through 177' Processing helix chain 'J' and resid 179 through 193 removed outlier: 4.042A pdb=" N ASN J 193 " --> pdb=" O ASP J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 209 removed outlier: 3.583A pdb=" N VAL J 205 " --> pdb=" O LYS J 201 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU J 206 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE J 208 " --> pdb=" O PHE J 204 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN J 209 " --> pdb=" O VAL J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 237 removed outlier: 4.023A pdb=" N GLU J 227 " --> pdb=" O GLU J 223 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE J 236 " --> pdb=" O LEU J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 274 removed outlier: 3.548A pdb=" N CYS J 266 " --> pdb=" O THR J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 309 removed outlier: 3.582A pdb=" N GLU J 309 " --> pdb=" O GLN J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 334 removed outlier: 3.705A pdb=" N SER J 334 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 345 through 356 removed outlier: 3.760A pdb=" N GLU J 351 " --> pdb=" O ASP J 347 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR J 352 " --> pdb=" O ASP J 348 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN J 354 " --> pdb=" O ASN J 350 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 392 removed outlier: 4.038A pdb=" N LYS J 391 " --> pdb=" O PHE J 387 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU J 392 " --> pdb=" O ALA J 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 387 through 392' Processing helix chain 'K' and resid 152 through 169 removed outlier: 3.692A pdb=" N ILE K 164 " --> pdb=" O THR K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 177 removed outlier: 4.098A pdb=" N GLU K 176 " --> pdb=" O ASP K 172 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS K 177 " --> pdb=" O TYR K 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 172 through 177' Processing helix chain 'K' and resid 179 through 192 removed outlier: 3.509A pdb=" N ARG K 185 " --> pdb=" O SER K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 207 removed outlier: 3.689A pdb=" N GLU K 206 " --> pdb=" O SER K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 224 Processing helix chain 'K' and resid 227 through 237 removed outlier: 3.544A pdb=" N GLU K 234 " --> pdb=" O ARG K 230 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER K 235 " --> pdb=" O LYS K 231 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE K 236 " --> pdb=" O LEU K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 274 removed outlier: 4.125A pdb=" N CYS K 266 " --> pdb=" O THR K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 309 removed outlier: 3.566A pdb=" N GLU K 309 " --> pdb=" O GLN K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 334 removed outlier: 3.854A pdb=" N LEU K 329 " --> pdb=" O THR K 325 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER K 334 " --> pdb=" O ILE K 330 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 355 removed outlier: 3.858A pdb=" N GLU K 351 " --> pdb=" O ASP K 347 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER K 355 " --> pdb=" O GLU K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 394 removed outlier: 4.140A pdb=" N LYS K 391 " --> pdb=" O PHE K 387 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU K 392 " --> pdb=" O ALA K 388 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE K 393 " --> pdb=" O ASP K 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 169 Processing helix chain 'L' and resid 172 through 177 removed outlier: 3.748A pdb=" N HIS L 177 " --> pdb=" O TYR L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 192 removed outlier: 4.026A pdb=" N ILE L 190 " --> pdb=" O LYS L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 209 removed outlier: 3.577A pdb=" N ILE L 208 " --> pdb=" O PHE L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 217 through 222 Processing helix chain 'L' and resid 224 through 237 removed outlier: 3.611A pdb=" N GLU L 234 " --> pdb=" O ARG L 230 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER L 235 " --> pdb=" O LYS L 231 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE L 236 " --> pdb=" O LEU L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 274 Processing helix chain 'L' and resid 295 through 309 removed outlier: 3.554A pdb=" N GLU L 309 " --> pdb=" O GLN L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 335 removed outlier: 4.358A pdb=" N LEU L 329 " --> pdb=" O THR L 325 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER L 334 " --> pdb=" O ILE L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 345 through 355 removed outlier: 3.572A pdb=" N GLU L 351 " --> pdb=" O ASP L 347 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN L 354 " --> pdb=" O ASN L 350 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER L 355 " --> pdb=" O GLU L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 386 through 393 removed outlier: 3.638A pdb=" N LYS L 391 " --> pdb=" O ALA L 388 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE L 393 " --> pdb=" O ILE L 390 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 236 removed outlier: 4.272A pdb=" N PHE M 236 " --> pdb=" O LEU M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 244 removed outlier: 3.562A pdb=" N SER M 244 " --> pdb=" O VAL M 241 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 274 removed outlier: 3.816A pdb=" N VAL M 263 " --> pdb=" O ASP M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 309 removed outlier: 3.617A pdb=" N GLU M 309 " --> pdb=" O GLN M 305 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 335 removed outlier: 4.143A pdb=" N LEU M 329 " --> pdb=" O THR M 325 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER M 334 " --> pdb=" O ILE M 330 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 354 removed outlier: 3.503A pdb=" N ASN M 354 " --> pdb=" O ASN M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 389 through 394 removed outlier: 3.734A pdb=" N ILE M 393 " --> pdb=" O ASP M 389 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 235 removed outlier: 3.581A pdb=" N LEU N 229 " --> pdb=" O ARG N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 274 removed outlier: 3.887A pdb=" N VAL N 263 " --> pdb=" O ASP N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 295 through 309 Processing helix chain 'N' and resid 325 through 335 removed outlier: 4.161A pdb=" N LEU N 329 " --> pdb=" O THR N 325 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER N 334 " --> pdb=" O ILE N 330 " (cutoff:3.500A) Processing helix chain 'N' and resid 345 through 356 Processing helix chain 'N' and resid 386 through 388 No H-bonds generated for 'chain 'N' and resid 386 through 388' Processing helix chain 'N' and resid 389 through 394 Processing helix chain 'O' and resid 226 through 237 removed outlier: 4.033A pdb=" N PHE O 236 " --> pdb=" O LEU O 232 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE O 237 " --> pdb=" O LYS O 233 " (cutoff:3.500A) Processing helix chain 'O' and resid 259 through 274 removed outlier: 3.712A pdb=" N VAL O 263 " --> pdb=" O ASP O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 295 through 309 Processing helix chain 'O' and resid 325 through 335 removed outlier: 4.166A pdb=" N LEU O 329 " --> pdb=" O THR O 325 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER O 334 " --> pdb=" O ILE O 330 " (cutoff:3.500A) Processing helix chain 'O' and resid 345 through 354 removed outlier: 3.667A pdb=" N ASN O 354 " --> pdb=" O ASN O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 388 through 394 removed outlier: 4.393A pdb=" N GLU O 392 " --> pdb=" O ALA O 388 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 237 removed outlier: 3.649A pdb=" N LEU P 229 " --> pdb=" O ARG P 225 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE P 236 " --> pdb=" O LEU P 232 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 243 removed outlier: 3.737A pdb=" N ASN P 242 " --> pdb=" O ARG P 238 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR P 243 " --> pdb=" O ARG P 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 238 through 243' Processing helix chain 'P' and resid 259 through 274 removed outlier: 4.114A pdb=" N VAL P 263 " --> pdb=" O ASP P 259 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP P 265 " --> pdb=" O LYS P 261 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 309 Processing helix chain 'P' and resid 327 through 332 Processing helix chain 'P' and resid 345 through 354 removed outlier: 3.687A pdb=" N ASN P 354 " --> pdb=" O ASN P 350 " (cutoff:3.500A) Processing helix chain 'P' and resid 386 through 388 No H-bonds generated for 'chain 'P' and resid 386 through 388' Processing helix chain 'P' and resid 389 through 394 Processing helix chain 'Q' and resid 226 through 236 removed outlier: 3.609A pdb=" N LYS Q 231 " --> pdb=" O GLU Q 227 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU Q 232 " --> pdb=" O TYR Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 259 through 274 removed outlier: 3.641A pdb=" N VAL Q 263 " --> pdb=" O ASP Q 259 " (cutoff:3.500A) Processing helix chain 'Q' and resid 295 through 309 Processing helix chain 'Q' and resid 325 through 335 removed outlier: 3.990A pdb=" N LEU Q 329 " --> pdb=" O THR Q 325 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER Q 334 " --> pdb=" O ILE Q 330 " (cutoff:3.500A) Processing helix chain 'Q' and resid 345 through 354 removed outlier: 3.618A pdb=" N ASN Q 354 " --> pdb=" O ASN Q 350 " (cutoff:3.500A) Processing helix chain 'Q' and resid 386 through 388 No H-bonds generated for 'chain 'Q' and resid 386 through 388' Processing helix chain 'Q' and resid 389 through 394 Processing helix chain 'R' and resid 225 through 237 removed outlier: 3.629A pdb=" N ARG R 230 " --> pdb=" O LYS R 226 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE R 236 " --> pdb=" O LEU R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 275 Processing helix chain 'R' and resid 295 through 309 Processing helix chain 'R' and resid 325 through 335 removed outlier: 3.847A pdb=" N LEU R 329 " --> pdb=" O THR R 325 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER R 334 " --> pdb=" O ILE R 330 " (cutoff:3.500A) Processing helix chain 'R' and resid 345 through 354 removed outlier: 3.781A pdb=" N ASN R 354 " --> pdb=" O ASN R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 389 through 394 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.565A pdb=" N LYS A 20 " --> pdb=" O VAL A 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 19 through 23 current: chain 'A' and resid 50 through 62 removed outlier: 6.945A pdb=" N VAL A 50 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS A 82 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A 52 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 80 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA A 54 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE A 78 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE A 56 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER A 76 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 85 " --> pdb=" O LYS A 82 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 85 through 88 current: chain 'B' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 19 through 23 current: chain 'B' and resid 50 through 62 removed outlier: 7.052A pdb=" N VAL B 50 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS B 82 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 52 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 80 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ALA B 54 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE B 78 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE B 56 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER B 76 " --> pdb=" O ILE B 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 85 through 88 current: chain 'C' and resid 19 through 26 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 19 through 26 current: chain 'C' and resid 50 through 62 removed outlier: 6.653A pdb=" N ALA C 51 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU C 80 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU C 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU C 74 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE C 59 " --> pdb=" O MET C 72 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET C 72 " --> pdb=" O PHE C 59 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE C 61 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS C 70 " --> pdb=" O ILE C 61 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 85 through 88 current: chain 'D' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 19 through 23 current: chain 'D' and resid 50 through 62 removed outlier: 6.950A pdb=" N VAL D 50 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS D 82 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU D 52 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU D 80 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA D 54 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE D 78 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE D 56 " --> pdb=" O SER D 76 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER D 76 " --> pdb=" O ILE D 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 85 through 88 current: chain 'E' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 19 through 23 current: chain 'E' and resid 50 through 62 removed outlier: 6.939A pdb=" N VAL E 50 " --> pdb=" O LYS E 82 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS E 82 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU E 52 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU E 80 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA E 54 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE E 78 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE E 56 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER E 76 " --> pdb=" O ILE E 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 85 through 88 current: chain 'F' and resid 19 through 26 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 19 through 26 current: chain 'F' and resid 50 through 62 removed outlier: 5.556A pdb=" N ILE F 56 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N SER F 76 " --> pdb=" O ILE F 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 70 through 76 current: chain 'F' and resid 85 through 88 Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 138 removed outlier: 4.652A pdb=" N SER A 125 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 137 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N THR A 123 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS A 146 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ILE A 483 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA A 148 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 426 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 184 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU A 378 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A 186 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 301 removed outlier: 3.876A pdb=" N ILE A 292 " --> pdb=" O ASP A 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 122 Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.541A pdb=" N SER B 530 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA B 148 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 147 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N SER B 465 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE B 149 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 185 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASN B 201 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASP B 379 " --> pdb=" O ASN B 201 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 203 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 292 through 295 Processing sheet with id=AA7, first strand: chain 'C' and resid 134 through 138 removed outlier: 7.815A pdb=" N VAL C 135 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE C 124 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA C 148 " --> pdb=" O ILE C 483 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE C 147 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER C 465 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE C 149 " --> pdb=" O SER C 465 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE C 185 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU C 426 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE C 187 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASN C 201 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASP C 379 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU C 203 " --> pdb=" O ASP C 379 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 284 through 285 Processing sheet with id=AA9, first strand: chain 'C' and resid 299 through 301 removed outlier: 4.054A pdb=" N ILE C 292 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 134 through 138 removed outlier: 7.895A pdb=" N VAL D 135 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE D 124 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE D 147 " --> pdb=" O LEU D 463 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 185 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLU D 426 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE D 187 " --> pdb=" O GLU D 426 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ASN D 201 " --> pdb=" O ILE D 377 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP D 379 " --> pdb=" O ASN D 201 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU D 203 " --> pdb=" O ASP D 379 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 299 through 301 removed outlier: 3.865A pdb=" N ILE D 292 " --> pdb=" O ASP D 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 138 removed outlier: 4.601A pdb=" N SER E 125 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL E 137 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR E 123 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA E 148 " --> pdb=" O ILE E 483 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE E 147 " --> pdb=" O LEU E 463 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER E 465 " --> pdb=" O ILE E 147 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE E 149 " --> pdb=" O SER E 465 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS E 183 " --> pdb=" O LEU E 422 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL E 424 " --> pdb=" O HIS E 183 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE E 185 " --> pdb=" O VAL E 424 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU E 426 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE E 187 " --> pdb=" O GLU E 426 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE E 184 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU E 378 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE E 186 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN E 201 " --> pdb=" O ILE E 375 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 298 through 301 removed outlier: 3.656A pdb=" N ASP E 295 " --> pdb=" O GLY E 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 134 through 138 removed outlier: 7.831A pdb=" N VAL F 135 " --> pdb=" O PHE F 124 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE F 124 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER F 530 " --> pdb=" O ILE F 521 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE F 521 " --> pdb=" O SER F 530 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE F 421 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU F 462 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE F 423 " --> pdb=" O LEU F 462 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ALA F 464 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR F 425 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE F 185 " --> pdb=" O VAL F 424 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU F 426 " --> pdb=" O ILE F 185 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE F 184 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU F 378 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE F 186 " --> pdb=" O LEU F 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 284 through 285 Processing sheet with id=AB7, first strand: chain 'F' and resid 299 through 301 removed outlier: 3.938A pdb=" N ILE F 292 " --> pdb=" O ASP F 318 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 313 through 314 removed outlier: 6.224A pdb=" N THR G 314 " --> pdb=" O PHE G 342 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE G 291 " --> pdb=" O ILE G 343 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA G 247 " --> pdb=" O GLU G 361 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N TYR G 363 " --> pdb=" O ALA G 247 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE G 249 " --> pdb=" O TYR G 363 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE G 365 " --> pdb=" O PHE G 249 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE G 251 " --> pdb=" O PHE G 365 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 212 through 213 removed outlier: 6.224A pdb=" N ALA H 247 " --> pdb=" O GLU H 361 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N TYR H 363 " --> pdb=" O ALA H 247 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE H 249 " --> pdb=" O TYR H 363 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE H 365 " --> pdb=" O PHE H 249 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE H 251 " --> pdb=" O PHE H 365 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG H 248 " --> pdb=" O PHE H 288 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU H 290 " --> pdb=" O ARG H 248 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE H 250 " --> pdb=" O LEU H 290 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N HIS H 292 " --> pdb=" O PHE H 250 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU H 252 " --> pdb=" O HIS H 292 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE H 291 " --> pdb=" O ILE H 343 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR H 314 " --> pdb=" O PHE H 342 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 313 through 314 removed outlier: 6.285A pdb=" N THR I 314 " --> pdb=" O PHE I 342 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU I 289 " --> pdb=" O ILE I 343 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG I 248 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU I 290 " --> pdb=" O ARG I 248 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE I 250 " --> pdb=" O LEU I 290 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N HIS I 292 " --> pdb=" O PHE I 250 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU I 252 " --> pdb=" O HIS I 292 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA I 247 " --> pdb=" O GLU I 361 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N TYR I 363 " --> pdb=" O ALA I 247 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE I 249 " --> pdb=" O TYR I 363 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHE I 365 " --> pdb=" O PHE I 249 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE I 251 " --> pdb=" O PHE I 365 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 313 through 314 removed outlier: 6.212A pdb=" N THR J 314 " --> pdb=" O PHE J 342 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU J 289 " --> pdb=" O ILE J 343 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG J 248 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU J 290 " --> pdb=" O ARG J 248 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE J 250 " --> pdb=" O LEU J 290 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N HIS J 292 " --> pdb=" O PHE J 250 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU J 252 " --> pdb=" O HIS J 292 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA J 247 " --> pdb=" O GLU J 361 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N TYR J 363 " --> pdb=" O ALA J 247 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE J 249 " --> pdb=" O TYR J 363 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N PHE J 365 " --> pdb=" O PHE J 249 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE J 251 " --> pdb=" O PHE J 365 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 313 through 314 removed outlier: 6.301A pdb=" N THR K 314 " --> pdb=" O PHE K 342 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE K 291 " --> pdb=" O ILE K 343 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA K 247 " --> pdb=" O GLU K 361 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N TYR K 363 " --> pdb=" O ALA K 247 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE K 249 " --> pdb=" O TYR K 363 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE K 365 " --> pdb=" O PHE K 249 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE K 251 " --> pdb=" O PHE K 365 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 313 through 314 removed outlier: 6.372A pdb=" N THR L 314 " --> pdb=" O PHE L 342 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE L 291 " --> pdb=" O ILE L 343 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS L 292 " --> pdb=" O LEU L 252 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 313 through 314 removed outlier: 5.799A pdb=" N THR M 314 " --> pdb=" O PHE M 342 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE M 291 " --> pdb=" O ILE M 343 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA M 247 " --> pdb=" O GLU M 361 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N TYR M 363 " --> pdb=" O ALA M 247 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE M 249 " --> pdb=" O TYR M 363 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE M 365 " --> pdb=" O PHE M 249 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE M 251 " --> pdb=" O PHE M 365 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 313 through 314 removed outlier: 6.052A pdb=" N THR N 314 " --> pdb=" O PHE N 342 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE N 291 " --> pdb=" O ILE N 343 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS N 292 " --> pdb=" O LEU N 252 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA N 247 " --> pdb=" O GLU N 361 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N TYR N 363 " --> pdb=" O ALA N 247 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE N 249 " --> pdb=" O TYR N 363 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE N 365 " --> pdb=" O PHE N 249 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE N 251 " --> pdb=" O PHE N 365 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 313 through 314 removed outlier: 6.076A pdb=" N THR O 314 " --> pdb=" O PHE O 342 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE O 291 " --> pdb=" O ILE O 343 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N VAL O 380 " --> pdb=" O LYS O 360 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL O 362 " --> pdb=" O VAL O 380 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE O 382 " --> pdb=" O VAL O 362 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN O 364 " --> pdb=" O ILE O 382 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 313 through 314 removed outlier: 6.166A pdb=" N THR P 314 " --> pdb=" O PHE P 342 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE P 291 " --> pdb=" O ILE P 343 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA P 247 " --> pdb=" O GLU P 361 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N TYR P 363 " --> pdb=" O ALA P 247 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE P 249 " --> pdb=" O TYR P 363 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE P 365 " --> pdb=" O PHE P 249 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE P 251 " --> pdb=" O PHE P 365 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N VAL P 380 " --> pdb=" O LYS P 360 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL P 362 " --> pdb=" O VAL P 380 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE P 382 " --> pdb=" O VAL P 362 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN P 364 " --> pdb=" O ILE P 382 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 313 through 314 removed outlier: 5.895A pdb=" N THR Q 314 " --> pdb=" O PHE Q 342 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE Q 291 " --> pdb=" O ILE Q 343 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA Q 247 " --> pdb=" O GLU Q 361 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N TYR Q 363 " --> pdb=" O ALA Q 247 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE Q 249 " --> pdb=" O TYR Q 363 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE Q 365 " --> pdb=" O PHE Q 249 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE Q 251 " --> pdb=" O PHE Q 365 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'R' and resid 313 through 314 removed outlier: 5.958A pdb=" N THR R 314 " --> pdb=" O PHE R 342 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE R 291 " --> pdb=" O ILE R 343 " (cutoff:3.500A) 1679 hydrogen bonds defined for protein. 4794 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: 16.70 Time building geometry restraints manager: 10.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15151 1.34 - 1.46: 9571 1.46 - 1.58: 25161 1.58 - 1.70: 74 1.70 - 1.82: 114 Bond restraints: 50071 Sorted by residual: bond pdb=" O3A ANP B 601 " pdb=" PB ANP B 601 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" O3A ANP D 601 " pdb=" PB ANP D 601 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" O3A ANP C 601 " pdb=" PB ANP C 601 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" N3B ANP D 601 " pdb=" PG ANP D 601 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" N3B ANP C 601 " pdb=" PG ANP C 601 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.62e+01 ... (remaining 50066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 67272 4.03 - 8.05: 395 8.05 - 12.08: 34 12.08 - 16.11: 2 16.11 - 20.13: 4 Bond angle restraints: 67707 Sorted by residual: angle pdb=" CA PRO A 265 " pdb=" N PRO A 265 " pdb=" CD PRO A 265 " ideal model delta sigma weight residual 112.00 98.60 13.40 1.40e+00 5.10e-01 9.16e+01 angle pdb=" CG1 ILE G 237 " pdb=" CB ILE G 237 " pdb=" CG2 ILE G 237 " ideal model delta sigma weight residual 110.70 90.57 20.13 3.00e+00 1.11e-01 4.50e+01 angle pdb=" PB ANP C 601 " pdb=" N3B ANP C 601 " pdb=" PG ANP C 601 " ideal model delta sigma weight residual 126.95 107.39 19.56 3.00e+00 1.11e-01 4.25e+01 angle pdb=" PB ANP B 601 " pdb=" N3B ANP B 601 " pdb=" PG ANP B 601 " ideal model delta sigma weight residual 126.95 108.74 18.21 3.00e+00 1.11e-01 3.69e+01 angle pdb=" PB ANP D 601 " pdb=" N3B ANP D 601 " pdb=" PG ANP D 601 " ideal model delta sigma weight residual 126.95 110.08 16.87 3.00e+00 1.11e-01 3.16e+01 ... (remaining 67702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.15: 28880 34.15 - 68.29: 1382 68.29 - 102.44: 95 102.44 - 136.59: 3 136.59 - 170.73: 4 Dihedral angle restraints: 30364 sinusoidal: 12934 harmonic: 17430 Sorted by residual: dihedral pdb=" CA LYS C 408 " pdb=" C LYS C 408 " pdb=" N ILE C 409 " pdb=" CA ILE C 409 " ideal model delta harmonic sigma weight residual 180.00 143.91 36.09 0 5.00e+00 4.00e-02 5.21e+01 dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 109.44 -169.45 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O1B ADP F 601 " pdb=" O3A ADP F 601 " pdb=" PB ADP F 601 " pdb=" PA ADP F 601 " ideal model delta sinusoidal sigma weight residual -60.00 85.73 -145.73 1 2.00e+01 2.50e-03 4.38e+01 ... (remaining 30361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 6737 0.088 - 0.175: 610 0.175 - 0.263: 19 0.263 - 0.350: 9 0.350 - 0.438: 2 Chirality restraints: 7377 Sorted by residual: chirality pdb=" CB VAL D 383 " pdb=" CA VAL D 383 " pdb=" CG1 VAL D 383 " pdb=" CG2 VAL D 383 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CB ILE E 544 " pdb=" CA ILE E 544 " pdb=" CG1 ILE E 544 " pdb=" CG2 ILE E 544 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA LYS E 287 " pdb=" N LYS E 287 " pdb=" C LYS E 287 " pdb=" CB LYS E 287 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 7374 not shown) Planarity restraints: 8640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 253 " 0.082 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO F 254 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO F 254 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO F 254 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR Q 325 " 0.077 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO Q 326 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO Q 326 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO Q 326 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 419 " -0.073 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO F 420 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO F 420 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO F 420 " -0.060 5.00e-02 4.00e+02 ... (remaining 8637 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 649 2.61 - 3.18: 39814 3.18 - 3.76: 79370 3.76 - 4.33: 114616 4.33 - 4.90: 185634 Nonbonded interactions: 420083 Sorted by model distance: nonbonded pdb=" OG SER D 158 " pdb="MG MG D 602 " model vdw 2.039 2.170 nonbonded pdb=" O2G ANP D 601 " pdb="MG MG D 602 " model vdw 2.053 2.170 nonbonded pdb=" OG SER B 158 " pdb="MG MG B 602 " model vdw 2.054 2.170 nonbonded pdb=" OG SER C 158 " pdb="MG MG C 602 " model vdw 2.055 2.170 nonbonded pdb=" O1B ANP B 601 " pdb="MG MG B 602 " model vdw 2.071 2.170 ... (remaining 420078 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 502 or resid 507 through 571 or resid 602)) selection = (chain 'B' and (resid 5 through 502 or resid 507 through 571 or resid 602)) selection = (chain 'C' and (resid 5 through 502 or resid 507 through 571 or resid 602)) selection = (chain 'D' and (resid 5 through 571 or resid 602)) selection = (chain 'E' and (resid 5 through 502 or resid 507 through 571 or resid 602)) selection = (chain 'F' and (resid 5 through 502 or resid 507 through 571 or resid 602)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and ((resid 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 through 394)) selection = (chain 'N' and ((resid 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 through 394)) selection = (chain 'O' and ((resid 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 through 394)) selection = (chain 'P' and ((resid 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 through 394)) selection = chain 'Q' selection = (chain 'R' and ((resid 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 through 394)) } 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.440 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 78.920 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.168 50071 Z= 0.288 Angle : 0.806 20.132 67707 Z= 0.416 Chirality : 0.051 0.438 7377 Planarity : 0.007 0.124 8640 Dihedral : 18.549 170.734 19042 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.60 % Allowed : 30.09 % Favored : 69.31 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.10), residues: 5849 helix: -2.44 (0.08), residues: 2130 sheet: 0.06 (0.17), residues: 902 loop : -0.86 (0.11), residues: 2817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 556 HIS 0.009 0.001 HIS K 292 PHE 0.052 0.002 PHE G 184 TYR 0.029 0.002 TYR J 366 ARG 0.021 0.001 ARG F 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 758 time to evaluate : 4.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7089 (mm-30) REVERT: A 180 ASN cc_start: 0.7939 (p0) cc_final: 0.7653 (p0) REVERT: A 467 ARG cc_start: 0.8101 (ttp-110) cc_final: 0.7781 (mtm-85) REVERT: C 64 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7798 (ptpp) REVERT: C 205 VAL cc_start: 0.8598 (t) cc_final: 0.8050 (t) REVERT: D 188 ASP cc_start: 0.7985 (p0) cc_final: 0.7778 (p0) REVERT: E 285 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8812 (ptmt) REVERT: G 244 SER cc_start: 0.9043 (OUTLIER) cc_final: 0.8786 (m) REVERT: I 214 LEU cc_start: 0.7886 (mm) cc_final: 0.7608 (mt) REVERT: L 156 GLN cc_start: 0.5854 (pm20) cc_final: 0.5358 (pm20) REVERT: M 233 LYS cc_start: 0.7670 (tttt) cc_final: 0.7403 (tmtt) REVERT: O 269 LYS cc_start: 0.8817 (tptp) cc_final: 0.8586 (tptm) REVERT: O 369 ASN cc_start: 0.7446 (m110) cc_final: 0.7161 (m-40) outliers start: 33 outliers final: 6 residues processed: 783 average time/residue: 1.3279 time to fit residues: 1290.9483 Evaluate side-chains 635 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 625 time to evaluate : 4.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain O residue 334 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 493 optimal weight: 6.9990 chunk 442 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 457 optimal weight: 6.9990 chunk 177 optimal weight: 0.3980 chunk 278 optimal weight: 4.9990 chunk 340 optimal weight: 20.0000 chunk 530 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 GLN A 289 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN C 232 HIS C 480 ASN D 144 ASN D 466 GLN ** D 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 181 ASN E 195 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 HIS E 478 GLN F 119 ASN F 233 ASN F 245 ASN F 249 HIS F 308 HIS F 509 ASN ** H 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 341 GLN I 344 ASN I 354 ASN ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 376 GLN L 221 GLN P 255 GLN P 292 HIS ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 271 GLN Q 276 ASN Q 335 ASN ** Q 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 304 ASN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.156568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119452 restraints weight = 59607.770| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.97 r_work: 0.3276 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 50071 Z= 0.413 Angle : 0.642 11.340 67707 Z= 0.338 Chirality : 0.048 0.275 7377 Planarity : 0.005 0.074 8640 Dihedral : 9.874 175.013 6766 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.46 % Allowed : 25.65 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.10), residues: 5849 helix: -0.70 (0.10), residues: 2282 sheet: -0.17 (0.17), residues: 926 loop : -0.70 (0.11), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 274 HIS 0.007 0.001 HIS E 405 PHE 0.026 0.002 PHE B 385 TYR 0.015 0.002 TYR E 276 ARG 0.010 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 299 poor density : 689 time to evaluate : 4.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8012 (tm) REVERT: A 62 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: A 74 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8157 (mm-30) REVERT: A 104 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8129 (mtpp) REVERT: A 106 ASP cc_start: 0.8542 (m-30) cc_final: 0.8277 (m-30) REVERT: A 231 ASP cc_start: 0.6978 (t70) cc_final: 0.6704 (t70) REVERT: A 309 ARG cc_start: 0.8492 (ptm160) cc_final: 0.8024 (ptm160) REVERT: A 332 PHE cc_start: 0.8559 (t80) cc_final: 0.8338 (t80) REVERT: A 335 ARG cc_start: 0.7386 (mtm-85) cc_final: 0.6920 (mtt-85) REVERT: A 353 SER cc_start: 0.9107 (OUTLIER) cc_final: 0.8751 (m) REVERT: A 377 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8635 (mm) REVERT: A 436 ASP cc_start: 0.6927 (OUTLIER) cc_final: 0.6642 (t0) REVERT: A 467 ARG cc_start: 0.8415 (ttp-110) cc_final: 0.8038 (mtp180) REVERT: A 566 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: B 74 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8375 (mp0) REVERT: B 88 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8518 (ttp-110) REVERT: B 132 LYS cc_start: 0.8609 (mtmm) cc_final: 0.8230 (mptt) REVERT: B 301 LYS cc_start: 0.7936 (ttpt) cc_final: 0.7373 (tppt) REVERT: B 466 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: B 482 PHE cc_start: 0.7984 (m-80) cc_final: 0.7649 (m-80) REVERT: B 533 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8187 (tmtm) REVERT: B 555 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7679 (mm-30) REVERT: B 566 GLU cc_start: 0.8149 (pp20) cc_final: 0.7745 (pt0) REVERT: C 30 LYS cc_start: 0.8418 (tppt) cc_final: 0.8030 (mtpp) REVERT: C 52 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8770 (mp) REVERT: C 64 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7764 (mptt) REVERT: C 113 SER cc_start: 0.8163 (OUTLIER) cc_final: 0.7926 (m) REVERT: C 118 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8429 (mp) REVERT: C 230 ASN cc_start: 0.7652 (m-40) cc_final: 0.7399 (m-40) REVERT: C 394 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8474 (tt) REVERT: C 408 LYS cc_start: 0.8561 (ptmt) cc_final: 0.8259 (ptpp) REVERT: C 463 LEU cc_start: 0.9096 (tp) cc_final: 0.8880 (mp) REVERT: D 129 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7768 (mp) REVERT: D 294 SER cc_start: 0.8813 (OUTLIER) cc_final: 0.8585 (p) REVERT: D 482 PHE cc_start: 0.8188 (m-80) cc_final: 0.7823 (m-80) REVERT: D 490 PRO cc_start: 0.7980 (Cg_exo) cc_final: 0.7612 (Cg_endo) REVERT: D 563 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8207 (mptp) REVERT: E 7 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8614 (tp) REVERT: E 74 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: E 263 HIS cc_start: 0.8015 (p-80) cc_final: 0.6956 (m-70) REVERT: E 312 LYS cc_start: 0.8131 (mmtm) cc_final: 0.7800 (mmpt) REVERT: E 411 ARG cc_start: 0.6979 (mtp180) cc_final: 0.6706 (mmm160) REVERT: E 417 GLN cc_start: 0.6103 (OUTLIER) cc_final: 0.3794 (tm130) REVERT: E 562 ASP cc_start: 0.8313 (m-30) cc_final: 0.8064 (m-30) REVERT: F 64 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8263 (mttp) REVERT: F 70 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8341 (tttm) REVERT: F 104 LYS cc_start: 0.8029 (mttt) cc_final: 0.7618 (mmtp) REVERT: F 174 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: F 194 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7722 (tm-30) REVERT: F 235 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7503 (mtm110) REVERT: F 441 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7858 (ptt90) REVERT: G 261 LYS cc_start: 0.8287 (tppt) cc_final: 0.7970 (tppt) REVERT: H 164 ILE cc_start: 0.6281 (OUTLIER) cc_final: 0.5594 (tt) REVERT: H 212 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7103 (mttm) REVERT: H 238 ARG cc_start: 0.7863 (ttp-110) cc_final: 0.7547 (mtm180) REVERT: H 327 LYS cc_start: 0.8295 (ttpp) cc_final: 0.8087 (ttpp) REVERT: H 383 GLN cc_start: 0.8845 (tt0) cc_final: 0.8542 (tt0) REVERT: I 389 ASP cc_start: 0.7227 (m-30) cc_final: 0.6828 (m-30) REVERT: J 261 LYS cc_start: 0.7723 (ttmm) cc_final: 0.7214 (mmtm) REVERT: L 156 GLN cc_start: 0.5431 (pm20) cc_final: 0.4245 (pm20) REVERT: L 356 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8470 (mm) REVERT: M 229 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7404 (tp) REVERT: M 233 LYS cc_start: 0.7515 (tttt) cc_final: 0.6597 (tmtt) REVERT: M 280 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6473 (ttt-90) REVERT: M 283 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.6912 (mtp85) REVERT: M 299 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8674 (tp) REVERT: M 337 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8331 (mm-30) REVERT: N 314 THR cc_start: 0.8931 (p) cc_final: 0.8580 (t) REVERT: N 376 GLN cc_start: 0.8717 (pm20) cc_final: 0.8485 (pm20) REVERT: O 361 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8605 (mt-10) REVERT: O 369 ASN cc_start: 0.8012 (m110) cc_final: 0.7494 (m-40) REVERT: Q 237 ILE cc_start: 0.5280 (OUTLIER) cc_final: 0.5043 (mm) REVERT: Q 299 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8524 (tm) REVERT: R 228 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.5778 (p90) REVERT: R 392 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7744 (mt-10) outliers start: 299 outliers final: 104 residues processed: 915 average time/residue: 1.2674 time to fit residues: 1452.9739 Evaluate side-chains 731 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 588 time to evaluate : 4.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 467 ARG Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 235 ARG Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 441 ARG Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 567 GLN Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 212 LYS Chi-restraints excluded: chain H residue 236 PHE Chi-restraints excluded: chain H residue 325 THR Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 325 THR Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 265 ASP Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 273 ASN Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 356 ILE Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 280 ARG Chi-restraints excluded: chain M residue 283 ARG Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 360 LYS Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 272 SER Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 330 ILE Chi-restraints excluded: chain P residue 375 SER Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 244 SER Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 314 THR Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain R residue 392 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 377 optimal weight: 4.9990 chunk 549 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 368 optimal weight: 9.9990 chunk 340 optimal weight: 0.0000 chunk 211 optimal weight: 0.0270 chunk 49 optimal weight: 0.9990 chunk 355 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 overall best weight: 0.7646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 48 GLN ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 ASN D 245 ASN ** D 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN E 47 ASN E 181 ASN E 201 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 233 ASN F 245 ASN H 379 GLN I 177 HIS I 344 ASN ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 GLN ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 383 GLN M 379 GLN N 379 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 364 GLN ** Q 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 379 GLN R 271 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.159734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124962 restraints weight = 59977.231| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.98 r_work: 0.3322 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 50071 Z= 0.165 Angle : 0.493 9.960 67707 Z= 0.261 Chirality : 0.043 0.207 7377 Planarity : 0.004 0.065 8640 Dihedral : 9.309 172.045 6755 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.95 % Allowed : 26.07 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.11), residues: 5849 helix: 0.02 (0.11), residues: 2287 sheet: -0.20 (0.17), residues: 881 loop : -0.57 (0.12), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 274 HIS 0.005 0.001 HIS D 190 PHE 0.022 0.001 PHE G 184 TYR 0.017 0.001 TYR K 220 ARG 0.007 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 670 time to evaluate : 4.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8144 (mm-30) REVERT: A 231 ASP cc_start: 0.7209 (t70) cc_final: 0.6945 (t70) REVERT: A 306 ASN cc_start: 0.7901 (t0) cc_final: 0.7516 (t0) REVERT: A 445 GLU cc_start: 0.8141 (tp30) cc_final: 0.7854 (tt0) REVERT: A 467 ARG cc_start: 0.8422 (ttp-110) cc_final: 0.7888 (mtm-85) REVERT: A 566 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: B 74 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8334 (mp0) REVERT: B 99 LYS cc_start: 0.8678 (pptt) cc_final: 0.8463 (pptt) REVERT: B 132 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8158 (mptt) REVERT: B 299 ASN cc_start: 0.8365 (m110) cc_final: 0.8065 (m-40) REVERT: B 301 LYS cc_start: 0.7898 (ttpt) cc_final: 0.7352 (tppt) REVERT: B 418 ASP cc_start: 0.6341 (OUTLIER) cc_final: 0.6123 (m-30) REVERT: B 463 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8628 (mp) REVERT: B 466 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: B 482 PHE cc_start: 0.7947 (m-80) cc_final: 0.7552 (m-80) REVERT: B 548 TYR cc_start: 0.8908 (m-80) cc_final: 0.8069 (t80) REVERT: B 555 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7524 (mm-30) REVERT: C 30 LYS cc_start: 0.8203 (tppt) cc_final: 0.7841 (mtpp) REVERT: C 64 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7901 (mttp) REVERT: C 118 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8369 (mp) REVERT: C 141 ARG cc_start: 0.8690 (mtt-85) cc_final: 0.8473 (mtp180) REVERT: C 205 VAL cc_start: 0.8698 (t) cc_final: 0.8228 (t) REVERT: C 282 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8664 (m110) REVERT: C 386 GLU cc_start: 0.8119 (mp0) cc_final: 0.7913 (mm-30) REVERT: C 394 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8417 (tt) REVERT: C 408 LYS cc_start: 0.8401 (ptmt) cc_final: 0.8108 (ptpp) REVERT: D 129 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7771 (mp) REVERT: D 194 GLU cc_start: 0.7795 (tt0) cc_final: 0.7290 (mt-10) REVERT: D 228 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6640 (pm20) REVERT: D 294 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8537 (p) REVERT: D 386 GLU cc_start: 0.7916 (mp0) cc_final: 0.7716 (mp0) REVERT: D 473 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7822 (mm-30) REVERT: D 482 PHE cc_start: 0.8215 (m-80) cc_final: 0.7792 (m-80) REVERT: D 490 PRO cc_start: 0.7811 (Cg_exo) cc_final: 0.7485 (Cg_endo) REVERT: D 545 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7771 (m-30) REVERT: D 555 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7981 (mm-30) REVERT: D 563 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8103 (mmtm) REVERT: D 570 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7909 (mppt) REVERT: E 7 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8537 (tp) REVERT: E 64 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7876 (mttp) REVERT: E 194 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: E 263 HIS cc_start: 0.8026 (p-80) cc_final: 0.6989 (m-70) REVERT: E 386 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8683 (mp0) REVERT: E 411 ARG cc_start: 0.7083 (mtp180) cc_final: 0.6711 (mmm160) REVERT: E 562 ASP cc_start: 0.8335 (m-30) cc_final: 0.8099 (m-30) REVERT: F 70 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8331 (tttm) REVERT: F 104 LYS cc_start: 0.8044 (mttt) cc_final: 0.7625 (mmtp) REVERT: F 174 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: F 180 ASN cc_start: 0.9014 (p0) cc_final: 0.8783 (p0) REVERT: F 401 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8438 (mt-10) REVERT: F 441 ARG cc_start: 0.8312 (ppt90) cc_final: 0.8023 (ppt90) REVERT: G 261 LYS cc_start: 0.8241 (tppt) cc_final: 0.8016 (tppt) REVERT: G 265 ASP cc_start: 0.8120 (m-30) cc_final: 0.7897 (m-30) REVERT: G 345 ASP cc_start: 0.7832 (m-30) cc_final: 0.7357 (p0) REVERT: H 164 ILE cc_start: 0.6376 (OUTLIER) cc_final: 0.5683 (tt) REVERT: H 212 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.7046 (mttm) REVERT: H 231 LYS cc_start: 0.7870 (mmmm) cc_final: 0.7427 (ptpt) REVERT: H 238 ARG cc_start: 0.7836 (ttp-110) cc_final: 0.7534 (mtm180) REVERT: H 327 LYS cc_start: 0.8359 (ttpp) cc_final: 0.8148 (ttpp) REVERT: H 383 GLN cc_start: 0.8684 (tt0) cc_final: 0.8365 (tt0) REVERT: I 153 PHE cc_start: 0.2359 (OUTLIER) cc_final: 0.1670 (t80) REVERT: I 214 LEU cc_start: 0.8234 (mm) cc_final: 0.7998 (mt) REVERT: I 301 GLU cc_start: 0.8430 (tp30) cc_final: 0.8173 (tm-30) REVERT: I 389 ASP cc_start: 0.7254 (m-30) cc_final: 0.6826 (m-30) REVERT: J 317 TYR cc_start: 0.9208 (m-80) cc_final: 0.8984 (m-80) REVERT: L 156 GLN cc_start: 0.5500 (pm20) cc_final: 0.4464 (pm20) REVERT: M 233 LYS cc_start: 0.7417 (tttt) cc_final: 0.6573 (tmtt) REVERT: M 299 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8627 (tp) REVERT: M 348 ASP cc_start: 0.9002 (m-30) cc_final: 0.8793 (m-30) REVERT: N 279 LYS cc_start: 0.8350 (pptt) cc_final: 0.7931 (mppt) REVERT: N 314 THR cc_start: 0.8691 (p) cc_final: 0.8484 (t) REVERT: N 331 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: N 376 GLN cc_start: 0.8789 (pm20) cc_final: 0.8531 (pm20) REVERT: N 392 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: O 227 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5706 (pp20) REVERT: O 242 ASN cc_start: 0.6733 (m-40) cc_final: 0.6393 (m-40) REVERT: O 301 GLU cc_start: 0.8760 (tp30) cc_final: 0.8328 (tp30) REVERT: O 314 THR cc_start: 0.8954 (p) cc_final: 0.8577 (t) REVERT: O 369 ASN cc_start: 0.7956 (m110) cc_final: 0.7485 (m-40) REVERT: Q 302 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8795 (tp) REVERT: Q 392 GLU cc_start: 0.8665 (mp0) cc_final: 0.8357 (mt-10) REVERT: R 228 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.5726 (p90) REVERT: R 351 GLU cc_start: 0.8053 (tt0) cc_final: 0.7817 (tt0) REVERT: R 392 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7614 (mt-10) outliers start: 216 outliers final: 80 residues processed: 829 average time/residue: 1.2665 time to fit residues: 1320.5440 Evaluate side-chains 681 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 568 time to evaluate : 4.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 555 GLU Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 194 GLU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 567 GLN Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 212 LYS Chi-restraints excluded: chain H residue 236 PHE Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain H residue 379 GLN Chi-restraints excluded: chain I residue 153 PHE Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain J residue 281 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 373 ILE Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 259 ASP Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 256 ASP Chi-restraints excluded: chain N residue 331 GLU Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 392 GLU Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 257 LYS Chi-restraints excluded: chain O residue 310 ASP Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 330 ILE Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 392 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 158 optimal weight: 4.9990 chunk 567 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 263 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 475 optimal weight: 0.6980 chunk 497 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 441 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 ASN D 245 ASN ** D 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 47 ASN E 67 GLN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 233 ASN ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 GLN ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN K 379 GLN K 383 GLN L 305 GLN M 379 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 364 GLN Q 273 ASN ** Q 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113472 restraints weight = 60203.897| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.87 r_work: 0.3204 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 50071 Z= 0.268 Angle : 0.525 9.005 67707 Z= 0.276 Chirality : 0.045 0.226 7377 Planarity : 0.004 0.059 8640 Dihedral : 9.301 174.881 6755 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.04 % Allowed : 24.92 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.11), residues: 5849 helix: 0.28 (0.11), residues: 2291 sheet: -0.45 (0.17), residues: 912 loop : -0.47 (0.12), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 274 HIS 0.005 0.001 HIS E 405 PHE 0.021 0.001 PHE G 184 TYR 0.017 0.001 TYR H 180 ARG 0.008 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 276 poor density : 613 time to evaluate : 4.242 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7804 (tm) REVERT: A 34 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8133 (pm20) REVERT: A 74 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8175 (mm-30) REVERT: A 194 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: A 306 ASN cc_start: 0.7907 (t0) cc_final: 0.7562 (t0) REVERT: A 309 ARG cc_start: 0.8371 (ptm160) cc_final: 0.7934 (ptm160) REVERT: A 377 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8559 (mm) REVERT: A 445 GLU cc_start: 0.7887 (tp30) cc_final: 0.7503 (tt0) REVERT: A 467 ARG cc_start: 0.8147 (ttp-110) cc_final: 0.7768 (mtp180) REVERT: A 473 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7922 (mm-30) REVERT: B 28 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6946 (tm-30) REVERT: B 64 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.7745 (mttp) REVERT: B 74 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8371 (mp0) REVERT: B 88 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8501 (ttp-110) REVERT: B 99 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8618 (pptt) REVERT: B 132 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8138 (mptt) REVERT: B 418 ASP cc_start: 0.6133 (OUTLIER) cc_final: 0.5913 (m-30) REVERT: B 427 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7875 (mm-30) REVERT: B 466 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: B 548 TYR cc_start: 0.8894 (m-80) cc_final: 0.7872 (t80) REVERT: C 30 LYS cc_start: 0.8065 (tppt) cc_final: 0.7862 (mttm) REVERT: C 64 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.7832 (mttp) REVERT: C 82 LYS cc_start: 0.8439 (mttp) cc_final: 0.8070 (mtpt) REVERT: C 113 SER cc_start: 0.8064 (OUTLIER) cc_final: 0.7827 (m) REVERT: C 141 ARG cc_start: 0.8612 (mtt-85) cc_final: 0.8292 (mtp85) REVERT: C 189 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8354 (pt) REVERT: C 205 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8260 (t) REVERT: C 258 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: C 394 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8272 (tt) REVERT: C 408 LYS cc_start: 0.8380 (ptmt) cc_final: 0.8069 (ptpp) REVERT: D 129 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7762 (mp) REVERT: D 206 ASP cc_start: 0.8145 (m-30) cc_final: 0.7582 (m-30) REVERT: D 258 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7771 (mm-30) REVERT: D 294 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8433 (p) REVERT: D 328 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.7949 (mttp) REVERT: D 427 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7094 (mt-10) REVERT: D 473 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: D 482 PHE cc_start: 0.8270 (m-80) cc_final: 0.7853 (m-80) REVERT: D 490 PRO cc_start: 0.7655 (Cg_exo) cc_final: 0.7334 (Cg_endo) REVERT: D 545 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: D 555 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7930 (mm-30) REVERT: D 563 LYS cc_start: 0.8379 (mmtp) cc_final: 0.8034 (mmtm) REVERT: D 570 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7734 (mppt) REVERT: E 7 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8449 (tp) REVERT: E 64 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7733 (mttp) REVERT: E 256 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8075 (p) REVERT: E 263 HIS cc_start: 0.7875 (p-80) cc_final: 0.6759 (m90) REVERT: E 411 ARG cc_start: 0.6909 (mtp180) cc_final: 0.6541 (mmm160) REVERT: E 430 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8242 (mtmt) REVERT: E 562 ASP cc_start: 0.8385 (m-30) cc_final: 0.8127 (m-30) REVERT: F 64 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8193 (mttp) REVERT: F 70 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8091 (tttm) REVERT: F 104 LYS cc_start: 0.7919 (mttt) cc_final: 0.7357 (mmtp) REVERT: F 173 GLN cc_start: 0.7437 (tt0) cc_final: 0.7202 (tt0) REVERT: F 174 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: F 328 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7319 (ptpt) REVERT: G 261 LYS cc_start: 0.8042 (tppt) cc_final: 0.7727 (tppt) REVERT: G 265 ASP cc_start: 0.8047 (m-30) cc_final: 0.7829 (m-30) REVERT: G 345 ASP cc_start: 0.7828 (m-30) cc_final: 0.7549 (m-30) REVERT: G 359 ARG cc_start: 0.8043 (ttt90) cc_final: 0.7671 (tmt-80) REVERT: H 231 LYS cc_start: 0.7741 (mmmm) cc_final: 0.7148 (ptpt) REVERT: H 238 ARG cc_start: 0.7791 (ttp-110) cc_final: 0.7406 (mtm180) REVERT: H 327 LYS cc_start: 0.8111 (ttpp) cc_final: 0.7857 (ttpp) REVERT: H 383 GLN cc_start: 0.8814 (tt0) cc_final: 0.8419 (tt0) REVERT: I 153 PHE cc_start: 0.2396 (OUTLIER) cc_final: 0.1760 (t80) REVERT: I 301 GLU cc_start: 0.8276 (tp30) cc_final: 0.8007 (tm-30) REVERT: I 389 ASP cc_start: 0.7185 (m-30) cc_final: 0.6659 (m-30) REVERT: J 317 TYR cc_start: 0.9144 (m-80) cc_final: 0.8864 (m-80) REVERT: K 373 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8442 (mm) REVERT: L 156 GLN cc_start: 0.5425 (pm20) cc_final: 0.4449 (pm20) REVERT: L 184 PHE cc_start: 0.6050 (t80) cc_final: 0.5825 (t80) REVERT: M 280 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6876 (ptm160) REVERT: M 299 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8482 (tp) REVERT: M 337 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8335 (mm-30) REVERT: M 385 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6866 (mppt) REVERT: N 279 LYS cc_start: 0.8293 (pptt) cc_final: 0.7801 (mppt) REVERT: N 314 THR cc_start: 0.8677 (p) cc_final: 0.8362 (t) REVERT: N 331 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: N 376 GLN cc_start: 0.8719 (pm20) cc_final: 0.8489 (pm20) REVERT: N 392 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: O 227 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5804 (pp20) REVERT: O 301 GLU cc_start: 0.8412 (tp30) cc_final: 0.8061 (tp30) REVERT: O 314 THR cc_start: 0.8972 (p) cc_final: 0.8530 (t) REVERT: O 369 ASN cc_start: 0.7910 (m110) cc_final: 0.7449 (m-40) REVERT: Q 237 ILE cc_start: 0.4950 (OUTLIER) cc_final: 0.4666 (mm) REVERT: Q 302 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8646 (tp) REVERT: Q 392 GLU cc_start: 0.8600 (mp0) cc_final: 0.8241 (mt-10) REVERT: R 228 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.5533 (p90) REVERT: R 237 ILE cc_start: 0.6172 (OUTLIER) cc_final: 0.5203 (tt) REVERT: R 392 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7523 (mt-10) outliers start: 276 outliers final: 125 residues processed: 826 average time/residue: 1.2536 time to fit residues: 1304.4083 Evaluate side-chains 730 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 562 time to evaluate : 4.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 467 ARG Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 555 GLU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 567 GLN Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain H residue 236 PHE Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain I residue 153 PHE Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain J residue 281 THR Chi-restraints excluded: chain J residue 325 THR Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 281 THR Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 373 ILE Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 280 ARG Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 385 LYS Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 256 ASP Chi-restraints excluded: chain N residue 331 GLU Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 360 LYS Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 392 GLU Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 269 LYS Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 375 SER Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 244 SER Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 314 THR Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 380 VAL Chi-restraints excluded: chain R residue 392 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 430 optimal weight: 0.3980 chunk 272 optimal weight: 1.9990 chunk 470 optimal weight: 0.5980 chunk 566 optimal weight: 20.0000 chunk 572 optimal weight: 3.9990 chunk 384 optimal weight: 1.9990 chunk 405 optimal weight: 1.9990 chunk 446 optimal weight: 0.9990 chunk 423 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 GLN B 67 GLN B 240 GLN ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 ASN D 240 GLN D 245 ASN ** D 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 567 GLN E 5 ASN E 47 ASN E 245 ASN F 119 ASN F 233 ASN ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 379 GLN ** H 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 GLN ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 ASN K 379 GLN K 383 GLN L 305 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 364 GLN Q 242 ASN ** Q 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 379 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110482 restraints weight = 58568.644| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.04 r_work: 0.3093 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 50071 Z= 0.175 Angle : 0.477 8.692 67707 Z= 0.251 Chirality : 0.043 0.218 7377 Planarity : 0.004 0.057 8640 Dihedral : 9.050 174.860 6753 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.46 % Allowed : 25.54 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.11), residues: 5849 helix: 0.52 (0.11), residues: 2297 sheet: -0.31 (0.17), residues: 876 loop : -0.43 (0.12), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 274 HIS 0.004 0.001 HIS D 190 PHE 0.023 0.001 PHE G 184 TYR 0.014 0.001 TYR H 180 ARG 0.007 0.000 ARG F 441 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 629 time to evaluate : 4.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: A 74 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8112 (mm-30) REVERT: A 231 ASP cc_start: 0.6442 (t70) cc_final: 0.6027 (t70) REVERT: A 306 ASN cc_start: 0.7803 (t0) cc_final: 0.7381 (t0) REVERT: A 309 ARG cc_start: 0.8181 (ptm160) cc_final: 0.7662 (ptm160) REVERT: A 445 GLU cc_start: 0.7627 (tp30) cc_final: 0.7068 (tt0) REVERT: A 467 ARG cc_start: 0.7803 (ttp-110) cc_final: 0.7463 (mtp180) REVERT: A 473 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7475 (mm-30) REVERT: B 7 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7876 (tp) REVERT: B 28 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6745 (tm-30) REVERT: B 74 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8131 (mp0) REVERT: B 88 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7832 (mtp85) REVERT: B 132 LYS cc_start: 0.8444 (mtmm) cc_final: 0.7897 (mptt) REVERT: B 299 ASN cc_start: 0.8256 (m110) cc_final: 0.7804 (m-40) REVERT: B 305 GLU cc_start: 0.7927 (mp0) cc_final: 0.7721 (mp0) REVERT: B 427 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7553 (mm-30) REVERT: B 466 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.7507 (mt0) REVERT: B 548 TYR cc_start: 0.8747 (m-80) cc_final: 0.7787 (t80) REVERT: B 553 ARG cc_start: 0.7913 (mtp-110) cc_final: 0.7484 (mtm-85) REVERT: C 15 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8339 (m) REVERT: C 25 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8311 (t70) REVERT: C 30 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7297 (mtpp) REVERT: C 64 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7655 (mttp) REVERT: C 82 LYS cc_start: 0.8209 (mttp) cc_final: 0.7790 (mtpt) REVERT: C 141 ARG cc_start: 0.8480 (mtt-85) cc_final: 0.8039 (mtp180) REVERT: C 157 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8110 (mtmt) REVERT: C 189 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7996 (pt) REVERT: C 205 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.8014 (t) REVERT: C 258 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: C 394 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8043 (tt) REVERT: C 408 LYS cc_start: 0.8086 (ptmt) cc_final: 0.7749 (ptpp) REVERT: C 495 TYR cc_start: 0.8365 (t80) cc_final: 0.7933 (t80) REVERT: D 65 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: D 129 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7602 (mp) REVERT: D 206 ASP cc_start: 0.8136 (m-30) cc_final: 0.7597 (m-30) REVERT: D 258 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7549 (mm-30) REVERT: D 294 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8250 (p) REVERT: D 328 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7654 (mttp) REVERT: D 344 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.6911 (mtt180) REVERT: D 427 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6877 (mt-10) REVERT: D 466 GLN cc_start: 0.7543 (tt0) cc_final: 0.7274 (tt0) REVERT: D 473 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7607 (mm-30) REVERT: D 482 PHE cc_start: 0.8055 (m-80) cc_final: 0.7593 (m-80) REVERT: D 490 PRO cc_start: 0.7260 (Cg_exo) cc_final: 0.6999 (Cg_endo) REVERT: D 545 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: D 555 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7756 (mm-30) REVERT: D 563 LYS cc_start: 0.8242 (mmtp) cc_final: 0.7893 (mmtm) REVERT: E 64 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7488 (mttp) REVERT: E 263 HIS cc_start: 0.7672 (p-80) cc_final: 0.6441 (m90) REVERT: E 386 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8423 (mp0) REVERT: E 401 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7764 (mm-30) REVERT: E 411 ARG cc_start: 0.6735 (mtp180) cc_final: 0.6393 (mmm160) REVERT: E 562 ASP cc_start: 0.8284 (m-30) cc_final: 0.7997 (m-30) REVERT: F 64 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7865 (mttp) REVERT: F 70 LYS cc_start: 0.8490 (ttmm) cc_final: 0.7866 (tttm) REVERT: F 104 LYS cc_start: 0.7759 (mttt) cc_final: 0.7344 (mmtp) REVERT: F 174 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6959 (pm20) REVERT: F 180 ASN cc_start: 0.9030 (p0) cc_final: 0.8815 (p0) REVERT: F 328 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7105 (ptpt) REVERT: F 370 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8189 (tttm) REVERT: F 401 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8050 (mt-10) REVERT: F 441 ARG cc_start: 0.7808 (ptt-90) cc_final: 0.7604 (ptt-90) REVERT: G 234 GLU cc_start: 0.7876 (pt0) cc_final: 0.7127 (mp0) REVERT: G 261 LYS cc_start: 0.7676 (tppt) cc_final: 0.7451 (tppt) REVERT: G 315 ASP cc_start: 0.8423 (p0) cc_final: 0.8138 (p0) REVERT: G 331 GLU cc_start: 0.8212 (pt0) cc_final: 0.8010 (pt0) REVERT: G 345 ASP cc_start: 0.7707 (m-30) cc_final: 0.7403 (m-30) REVERT: G 359 ARG cc_start: 0.7918 (ttt90) cc_final: 0.7521 (tmt-80) REVERT: H 231 LYS cc_start: 0.7548 (mmmm) cc_final: 0.7212 (ttmt) REVERT: H 238 ARG cc_start: 0.7694 (ttp-110) cc_final: 0.7319 (mmm-85) REVERT: H 327 LYS cc_start: 0.7787 (ttpp) cc_final: 0.7506 (ttpp) REVERT: H 383 GLN cc_start: 0.8549 (tt0) cc_final: 0.8182 (tt0) REVERT: I 153 PHE cc_start: 0.2351 (OUTLIER) cc_final: 0.1784 (t80) REVERT: I 214 LEU cc_start: 0.7824 (mm) cc_final: 0.7581 (mt) REVERT: I 301 GLU cc_start: 0.8087 (tp30) cc_final: 0.7794 (tm-30) REVERT: I 389 ASP cc_start: 0.7076 (m-30) cc_final: 0.6580 (m-30) REVERT: J 314 THR cc_start: 0.9130 (p) cc_final: 0.8717 (t) REVERT: K 373 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8323 (mm) REVERT: L 156 GLN cc_start: 0.5277 (pm20) cc_final: 0.4138 (pm20) REVERT: L 184 PHE cc_start: 0.5770 (t80) cc_final: 0.5542 (t80) REVERT: L 253 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: L 345 ASP cc_start: 0.7966 (p0) cc_final: 0.7723 (p0) REVERT: M 233 LYS cc_start: 0.7328 (tttt) cc_final: 0.6433 (tptm) REVERT: M 299 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8274 (tp) REVERT: N 279 LYS cc_start: 0.8138 (pptt) cc_final: 0.7612 (mppt) REVERT: N 314 THR cc_start: 0.8519 (p) cc_final: 0.8196 (t) REVERT: N 331 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: N 376 GLN cc_start: 0.8546 (pm20) cc_final: 0.8299 (pm20) REVERT: N 392 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: O 227 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5835 (pp20) REVERT: O 253 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: O 301 GLU cc_start: 0.8187 (tp30) cc_final: 0.7715 (tp30) REVERT: O 314 THR cc_start: 0.8832 (p) cc_final: 0.8367 (t) REVERT: O 369 ASN cc_start: 0.7894 (m110) cc_final: 0.7469 (m-40) REVERT: Q 302 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8370 (tp) REVERT: Q 392 GLU cc_start: 0.8478 (mp0) cc_final: 0.8140 (mt-10) REVERT: R 228 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.5457 (p90) REVERT: R 351 GLU cc_start: 0.7695 (tt0) cc_final: 0.7300 (tt0) REVERT: R 367 THR cc_start: 0.8692 (m) cc_final: 0.8350 (p) REVERT: R 392 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7733 (mp0) outliers start: 244 outliers final: 109 residues processed: 810 average time/residue: 1.2730 time to fit residues: 1293.4623 Evaluate side-chains 722 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 573 time to evaluate : 4.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 555 GLU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 567 GLN Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 379 GLN Chi-restraints excluded: chain H residue 236 PHE Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain I residue 153 PHE Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 281 THR Chi-restraints excluded: chain J residue 325 THR Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain K residue 153 PHE Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 153 PHE Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 253 GLU Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 256 ASP Chi-restraints excluded: chain N residue 331 GLU Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 392 GLU Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 272 SER Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 330 ILE Chi-restraints excluded: chain P residue 375 SER Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 392 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 163 optimal weight: 5.9990 chunk 332 optimal weight: 0.0770 chunk 371 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 136 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 403 optimal weight: 1.9990 chunk 567 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 chunk 325 optimal weight: 6.9990 overall best weight: 1.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN D 144 ASN D 245 ASN ** D 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 47 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 480 ASN F 119 ASN ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 369 ASN ** H 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 379 GLN ** H 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 ASN ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 GLN ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN K 383 GLN L 305 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 364 GLN Q 242 ASN Q 273 ASN ** Q 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 379 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.148713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109397 restraints weight = 58595.870| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.05 r_work: 0.3076 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 50071 Z= 0.200 Angle : 0.486 7.556 67707 Z= 0.255 Chirality : 0.043 0.208 7377 Planarity : 0.004 0.057 8640 Dihedral : 9.033 175.232 6752 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.09 % Allowed : 26.07 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.11), residues: 5849 helix: 0.62 (0.11), residues: 2305 sheet: -0.50 (0.17), residues: 905 loop : -0.38 (0.12), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 274 HIS 0.005 0.001 HIS J 177 PHE 0.022 0.001 PHE I 184 TYR 0.018 0.001 TYR J 366 ARG 0.007 0.000 ARG J 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 613 time to evaluate : 4.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8083 (pm20) REVERT: A 74 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8159 (mm-30) REVERT: A 231 ASP cc_start: 0.6501 (t70) cc_final: 0.6170 (t70) REVERT: A 306 ASN cc_start: 0.7709 (t0) cc_final: 0.7501 (t0) REVERT: A 309 ARG cc_start: 0.8181 (ptm160) cc_final: 0.7671 (ptm160) REVERT: A 445 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7087 (tt0) REVERT: A 467 ARG cc_start: 0.7757 (ttp-110) cc_final: 0.7484 (mtp180) REVERT: B 28 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: B 48 GLN cc_start: 0.8870 (mt0) cc_final: 0.8628 (mt0) REVERT: B 64 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7500 (mttp) REVERT: B 74 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8158 (mp0) REVERT: B 88 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7845 (mtp85) REVERT: B 132 LYS cc_start: 0.8452 (mtmm) cc_final: 0.7889 (mptt) REVERT: B 144 ASN cc_start: 0.8020 (t0) cc_final: 0.7752 (t0) REVERT: B 221 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7565 (tt0) REVERT: B 299 ASN cc_start: 0.8211 (m110) cc_final: 0.7747 (m-40) REVERT: B 418 ASP cc_start: 0.5935 (OUTLIER) cc_final: 0.5694 (m-30) REVERT: B 427 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7545 (mm-30) REVERT: B 466 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.7635 (mt0) REVERT: B 548 TYR cc_start: 0.8761 (m-80) cc_final: 0.7755 (t80) REVERT: B 553 ARG cc_start: 0.7917 (mtp-110) cc_final: 0.7427 (mtm-85) REVERT: B 562 ASP cc_start: 0.8333 (m-30) cc_final: 0.8128 (m-30) REVERT: C 15 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8391 (m) REVERT: C 30 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7291 (mtpp) REVERT: C 64 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7714 (mttp) REVERT: C 82 LYS cc_start: 0.8171 (mttp) cc_final: 0.7751 (mtpt) REVERT: C 141 ARG cc_start: 0.8500 (mtt-85) cc_final: 0.8041 (mtp180) REVERT: C 157 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8154 (mtmt) REVERT: C 189 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8017 (pt) REVERT: C 205 VAL cc_start: 0.8407 (OUTLIER) cc_final: 0.8057 (t) REVERT: C 394 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8092 (tt) REVERT: C 408 LYS cc_start: 0.8092 (ptmt) cc_final: 0.7750 (ptpp) REVERT: C 495 TYR cc_start: 0.8318 (t80) cc_final: 0.7998 (t80) REVERT: D 65 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: D 129 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7602 (mp) REVERT: D 206 ASP cc_start: 0.8118 (m-30) cc_final: 0.7599 (m-30) REVERT: D 258 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7572 (mm-30) REVERT: D 294 SER cc_start: 0.8647 (OUTLIER) cc_final: 0.8248 (p) REVERT: D 328 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7652 (mttp) REVERT: D 344 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6900 (mtt180) REVERT: D 466 GLN cc_start: 0.7519 (tt0) cc_final: 0.7286 (tt0) REVERT: D 473 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7613 (mm-30) REVERT: D 482 PHE cc_start: 0.8141 (m-80) cc_final: 0.7728 (m-80) REVERT: D 490 PRO cc_start: 0.7300 (Cg_exo) cc_final: 0.7044 (Cg_endo) REVERT: D 545 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7772 (m-30) REVERT: D 555 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: D 563 LYS cc_start: 0.8271 (mmtp) cc_final: 0.7940 (mmtm) REVERT: E 64 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7500 (mttp) REVERT: E 256 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8145 (p) REVERT: E 263 HIS cc_start: 0.7649 (p-80) cc_final: 0.6466 (m90) REVERT: E 312 LYS cc_start: 0.7555 (mmtp) cc_final: 0.7013 (mmpt) REVERT: E 386 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8385 (mp0) REVERT: E 411 ARG cc_start: 0.6773 (mtp180) cc_final: 0.6437 (mmm160) REVERT: E 430 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7912 (mtmt) REVERT: E 562 ASP cc_start: 0.8305 (m-30) cc_final: 0.8026 (m-30) REVERT: F 64 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7956 (mttp) REVERT: F 70 LYS cc_start: 0.8489 (ttmm) cc_final: 0.7851 (tttm) REVERT: F 104 LYS cc_start: 0.7748 (mttt) cc_final: 0.7346 (mmtp) REVERT: F 115 SER cc_start: 0.8600 (t) cc_final: 0.8375 (p) REVERT: F 328 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7086 (ptpt) REVERT: F 386 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: F 401 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8073 (mt-10) REVERT: F 441 ARG cc_start: 0.7836 (ptt-90) cc_final: 0.7532 (ptt-90) REVERT: G 231 LYS cc_start: 0.7599 (tptt) cc_final: 0.7283 (tttp) REVERT: G 234 GLU cc_start: 0.7836 (pt0) cc_final: 0.7123 (mp0) REVERT: G 331 GLU cc_start: 0.8188 (pt0) cc_final: 0.7892 (pt0) REVERT: G 345 ASP cc_start: 0.7727 (m-30) cc_final: 0.7415 (m-30) REVERT: G 359 ARG cc_start: 0.7924 (ttt90) cc_final: 0.7475 (tmt-80) REVERT: H 230 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7496 (ttp80) REVERT: H 231 LYS cc_start: 0.7660 (mmmm) cc_final: 0.7325 (ttmt) REVERT: H 238 ARG cc_start: 0.7721 (ttp-110) cc_final: 0.7191 (mtm180) REVERT: H 254 PHE cc_start: 0.8084 (t80) cc_final: 0.7849 (t80) REVERT: H 327 LYS cc_start: 0.7795 (ttpp) cc_final: 0.7523 (ttpp) REVERT: H 383 GLN cc_start: 0.8583 (tt0) cc_final: 0.8194 (tt0) REVERT: I 153 PHE cc_start: 0.2175 (OUTLIER) cc_final: 0.1593 (t80) REVERT: I 301 GLU cc_start: 0.8080 (tp30) cc_final: 0.7769 (tm-30) REVERT: I 383 GLN cc_start: 0.7416 (tm-30) cc_final: 0.7115 (tm-30) REVERT: I 389 ASP cc_start: 0.7077 (m-30) cc_final: 0.6499 (m-30) REVERT: J 314 THR cc_start: 0.9082 (p) cc_final: 0.8681 (t) REVERT: K 373 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8361 (mm) REVERT: L 156 GLN cc_start: 0.5355 (OUTLIER) cc_final: 0.4300 (pm20) REVERT: L 184 PHE cc_start: 0.5768 (t80) cc_final: 0.5558 (t80) REVERT: L 253 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: L 345 ASP cc_start: 0.7992 (p0) cc_final: 0.7759 (p0) REVERT: M 233 LYS cc_start: 0.7436 (tttt) cc_final: 0.6511 (tptm) REVERT: M 280 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6795 (ptm160) REVERT: M 299 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8286 (tp) REVERT: N 279 LYS cc_start: 0.8139 (pptt) cc_final: 0.7595 (mppt) REVERT: N 314 THR cc_start: 0.8504 (p) cc_final: 0.8180 (t) REVERT: N 376 GLN cc_start: 0.8526 (pm20) cc_final: 0.8272 (pm20) REVERT: N 392 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: O 227 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5886 (pp20) REVERT: O 301 GLU cc_start: 0.8099 (tp30) cc_final: 0.7641 (tp30) REVERT: O 314 THR cc_start: 0.8832 (p) cc_final: 0.8382 (t) REVERT: O 369 ASN cc_start: 0.7893 (m110) cc_final: 0.7453 (m-40) REVERT: P 327 LYS cc_start: 0.8046 (ttpp) cc_final: 0.7737 (ttmt) REVERT: Q 237 ILE cc_start: 0.4553 (OUTLIER) cc_final: 0.4306 (mm) REVERT: Q 302 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8379 (tp) REVERT: Q 392 GLU cc_start: 0.8483 (mp0) cc_final: 0.8155 (mt-10) REVERT: R 228 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.5625 (p90) REVERT: R 351 GLU cc_start: 0.7703 (tt0) cc_final: 0.7260 (tt0) REVERT: R 392 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7747 (mp0) outliers start: 224 outliers final: 121 residues processed: 785 average time/residue: 1.2519 time to fit residues: 1236.3548 Evaluate side-chains 746 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 584 time to evaluate : 4.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 467 ARG Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 555 GLU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 567 GLN Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 379 GLN Chi-restraints excluded: chain H residue 236 PHE Chi-restraints excluded: chain I residue 153 PHE Chi-restraints excluded: chain I residue 216 ASN Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 281 THR Chi-restraints excluded: chain J residue 325 THR Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain K residue 153 PHE Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 281 THR Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 153 PHE Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 253 GLU Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 280 ARG Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 389 ASP Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 256 ASP Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 392 GLU Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 272 SER Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 375 SER Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 244 SER Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 392 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 198 optimal weight: 3.9990 chunk 464 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 545 optimal weight: 7.9990 chunk 455 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 300 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 561 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 519 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN A 337 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN B 281 ASN C 5 ASN C 281 ASN C 282 ASN D 144 ASN D 230 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN E 47 ASN E 236 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN ** H 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 379 GLN I 216 ASN ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 305 GLN P 305 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 364 GLN Q 242 ASN ** Q 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 379 GLN R 305 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 369 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105036 restraints weight = 58789.308| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.06 r_work: 0.3007 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 50071 Z= 0.427 Angle : 0.601 8.230 67707 Z= 0.312 Chirality : 0.048 0.263 7377 Planarity : 0.004 0.058 8640 Dihedral : 9.493 178.045 6752 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.90 % Allowed : 25.26 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.11), residues: 5849 helix: 0.42 (0.11), residues: 2291 sheet: -0.59 (0.16), residues: 933 loop : -0.43 (0.12), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 274 HIS 0.007 0.001 HIS J 177 PHE 0.022 0.002 PHE I 184 TYR 0.024 0.002 TYR J 366 ARG 0.016 0.001 ARG I 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 268 poor density : 602 time to evaluate : 4.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7787 (tm) REVERT: A 28 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: A 62 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: A 74 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8283 (mm-30) REVERT: A 118 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8519 (tp) REVERT: A 231 ASP cc_start: 0.6573 (t70) cc_final: 0.6222 (t70) REVERT: A 284 ARG cc_start: 0.6663 (mtp85) cc_final: 0.6232 (mtp85) REVERT: A 309 ARG cc_start: 0.8292 (ptm160) cc_final: 0.8003 (ptm160) REVERT: A 377 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8568 (mm) REVERT: A 445 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: A 466 GLN cc_start: 0.8526 (pm20) cc_final: 0.8224 (pm20) REVERT: A 467 ARG cc_start: 0.7771 (ttp-110) cc_final: 0.7445 (mtp180) REVERT: B 28 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: B 64 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.7525 (mttp) REVERT: B 74 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8271 (mt-10) REVERT: B 88 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8556 (ttp-110) REVERT: B 221 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7658 (tt0) REVERT: B 337 GLN cc_start: 0.8055 (mt0) cc_final: 0.7810 (mt0) REVERT: B 427 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7846 (mm-30) REVERT: B 466 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: B 548 TYR cc_start: 0.8786 (m-80) cc_final: 0.7661 (t80) REVERT: B 553 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7576 (mtm-85) REVERT: B 562 ASP cc_start: 0.8553 (m-30) cc_final: 0.8327 (m-30) REVERT: C 64 LYS cc_start: 0.8715 (mtpp) cc_final: 0.7896 (mttp) REVERT: C 68 LYS cc_start: 0.8302 (ptmt) cc_final: 0.7787 (ptmm) REVERT: C 82 LYS cc_start: 0.8227 (mttp) cc_final: 0.7784 (mtpt) REVERT: C 119 ASN cc_start: 0.8354 (m-40) cc_final: 0.7938 (m-40) REVERT: C 141 ARG cc_start: 0.8521 (mtt-85) cc_final: 0.8035 (mtp85) REVERT: C 157 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8276 (mtmt) REVERT: C 205 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8162 (t) REVERT: C 258 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: C 394 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8005 (tt) REVERT: C 408 LYS cc_start: 0.8328 (ptmt) cc_final: 0.7982 (ptpp) REVERT: D 65 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: D 129 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7773 (mp) REVERT: D 206 ASP cc_start: 0.8199 (m-30) cc_final: 0.7727 (m-30) REVERT: D 328 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7844 (mttp) REVERT: D 344 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.6961 (mtt180) REVERT: D 466 GLN cc_start: 0.7569 (tt0) cc_final: 0.7339 (tt0) REVERT: D 473 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7647 (mm-30) REVERT: D 482 PHE cc_start: 0.8240 (m-80) cc_final: 0.7914 (m-80) REVERT: D 490 PRO cc_start: 0.7409 (Cg_exo) cc_final: 0.7115 (Cg_endo) REVERT: D 555 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: D 563 LYS cc_start: 0.8306 (mmtp) cc_final: 0.7967 (mmtm) REVERT: E 7 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8347 (tp) REVERT: E 20 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8300 (mttp) REVERT: E 64 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7604 (mttp) REVERT: E 67 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: E 256 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8171 (p) REVERT: E 263 HIS cc_start: 0.7629 (p-80) cc_final: 0.6494 (m90) REVERT: E 312 LYS cc_start: 0.7652 (mmtp) cc_final: 0.7154 (mmpt) REVERT: E 386 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: E 401 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7870 (mm-30) REVERT: E 411 ARG cc_start: 0.6808 (mtp180) cc_final: 0.6444 (mmm160) REVERT: E 430 LYS cc_start: 0.8428 (mtpt) cc_final: 0.8052 (mtmt) REVERT: E 436 ASP cc_start: 0.8221 (t0) cc_final: 0.8013 (t0) REVERT: E 516 GLU cc_start: 0.7266 (pm20) cc_final: 0.7032 (mp0) REVERT: E 562 ASP cc_start: 0.8408 (m-30) cc_final: 0.8174 (m-30) REVERT: F 64 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8138 (mttp) REVERT: F 104 LYS cc_start: 0.7796 (mttt) cc_final: 0.7208 (mmtp) REVERT: F 115 SER cc_start: 0.8610 (t) cc_final: 0.8374 (p) REVERT: F 235 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6844 (mmm160) REVERT: F 309 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6014 (mtt90) REVERT: F 328 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7266 (ptpt) REVERT: F 386 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: F 436 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7443 (t0) REVERT: F 441 ARG cc_start: 0.7769 (ptt-90) cc_final: 0.7511 (ptt-90) REVERT: G 345 ASP cc_start: 0.7852 (m-30) cc_final: 0.7522 (m-30) REVERT: G 359 ARG cc_start: 0.7987 (ttt90) cc_final: 0.7550 (tmt-80) REVERT: H 194 LYS cc_start: 0.4890 (OUTLIER) cc_final: 0.4557 (pmmt) REVERT: H 226 LYS cc_start: 0.8089 (mmmm) cc_final: 0.7411 (tmmm) REVERT: H 231 LYS cc_start: 0.7597 (mmmm) cc_final: 0.6963 (ptpt) REVERT: H 238 ARG cc_start: 0.7760 (ttp-110) cc_final: 0.7493 (mmm-85) REVERT: H 327 LYS cc_start: 0.7858 (ttpp) cc_final: 0.7651 (ttpp) REVERT: I 153 PHE cc_start: 0.2369 (OUTLIER) cc_final: 0.1685 (t80) REVERT: I 301 GLU cc_start: 0.8132 (tp30) cc_final: 0.7879 (tm-30) REVERT: I 377 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7457 (pp) REVERT: I 389 ASP cc_start: 0.7103 (m-30) cc_final: 0.6498 (m-30) REVERT: L 156 GLN cc_start: 0.5381 (pm20) cc_final: 0.4294 (pm20) REVERT: L 253 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: L 356 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8306 (mm) REVERT: L 376 GLN cc_start: 0.8354 (pm20) cc_final: 0.8144 (pm20) REVERT: M 233 LYS cc_start: 0.7379 (tttt) cc_final: 0.6466 (tptm) REVERT: M 280 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6866 (ptm160) REVERT: M 299 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8327 (tp) REVERT: M 337 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8119 (mm-30) REVERT: N 238 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6403 (ptt-90) REVERT: N 279 LYS cc_start: 0.8116 (pptt) cc_final: 0.7542 (mppt) REVERT: N 314 THR cc_start: 0.8741 (p) cc_final: 0.8320 (t) REVERT: N 376 GLN cc_start: 0.8442 (pm20) cc_final: 0.8166 (pm20) REVERT: N 392 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: O 227 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.5751 (pp20) REVERT: O 301 GLU cc_start: 0.8201 (tp30) cc_final: 0.7664 (tp30) REVERT: O 314 THR cc_start: 0.8844 (p) cc_final: 0.8398 (t) REVERT: O 369 ASN cc_start: 0.8048 (m110) cc_final: 0.7586 (m-40) REVERT: P 327 LYS cc_start: 0.8189 (ttpp) cc_final: 0.7838 (ttmt) REVERT: P 368 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8080 (tt0) REVERT: Q 237 ILE cc_start: 0.4625 (OUTLIER) cc_final: 0.4319 (mm) REVERT: Q 302 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8445 (tp) REVERT: Q 386 ASP cc_start: 0.7957 (m-30) cc_final: 0.7604 (p0) REVERT: Q 392 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8148 (mt-10) REVERT: R 228 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.5528 (p90) REVERT: R 279 LYS cc_start: 0.8132 (ptpt) cc_final: 0.7671 (ptmt) REVERT: R 351 GLU cc_start: 0.7744 (tt0) cc_final: 0.7380 (tt0) REVERT: R 369 ASN cc_start: 0.8090 (m-40) cc_final: 0.7870 (m110) REVERT: R 392 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7333 (mt-10) outliers start: 268 outliers final: 135 residues processed: 815 average time/residue: 1.2985 time to fit residues: 1322.6619 Evaluate side-chains 749 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 566 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 467 ARG Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 555 GLU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 537 CYS Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 235 ARG Chi-restraints excluded: chain F residue 309 ARG Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 436 ASP Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 567 GLN Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 194 LYS Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain I residue 153 PHE Chi-restraints excluded: chain I residue 216 ASN Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 281 THR Chi-restraints excluded: chain J residue 325 THR Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain K residue 153 PHE Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 281 THR Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 153 PHE Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 221 GLN Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 253 GLU Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 356 ILE Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 272 SER Chi-restraints excluded: chain M residue 280 ARG Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 392 GLU Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 269 LYS Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 375 SER Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 244 SER Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 314 THR Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain R residue 392 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 465 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 570 optimal weight: 5.9990 chunk 377 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 538 optimal weight: 4.9990 chunk 522 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 490 optimal weight: 2.9990 chunk 434 optimal weight: 20.0000 chunk 477 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN C 5 ASN C 282 ASN D 144 ASN D 245 ASN ** D 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN E 47 ASN E 240 GLN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 364 GLN H 379 GLN I 216 ASN I 344 ASN ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 379 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 364 GLN Q 242 ASN Q 273 ASN ** Q 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 379 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.146408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107328 restraints weight = 58478.640| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.01 r_work: 0.3052 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 50071 Z= 0.265 Angle : 0.522 8.092 67707 Z= 0.273 Chirality : 0.044 0.232 7377 Planarity : 0.004 0.058 8640 Dihedral : 9.244 174.686 6748 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.06 % Allowed : 26.64 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.11), residues: 5849 helix: 0.56 (0.11), residues: 2289 sheet: -0.59 (0.16), residues: 942 loop : -0.39 (0.12), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 274 HIS 0.006 0.001 HIS J 177 PHE 0.020 0.001 PHE I 184 TYR 0.018 0.001 TYR J 366 ARG 0.007 0.000 ARG J 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 586 time to evaluate : 4.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: A 74 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8179 (mm-30) REVERT: A 118 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8487 (tp) REVERT: A 231 ASP cc_start: 0.6608 (t70) cc_final: 0.6183 (t70) REVERT: A 309 ARG cc_start: 0.8385 (ptm160) cc_final: 0.7867 (ptm160) REVERT: A 335 ARG cc_start: 0.7125 (mtm-85) cc_final: 0.6863 (mtt-85) REVERT: A 445 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: A 466 GLN cc_start: 0.8540 (pm20) cc_final: 0.8199 (pm20) REVERT: A 467 ARG cc_start: 0.7800 (ttp-110) cc_final: 0.7491 (mtp180) REVERT: B 28 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: B 64 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7563 (mttp) REVERT: B 74 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8171 (mp0) REVERT: B 88 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8594 (ttp-110) REVERT: B 221 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7695 (tt0) REVERT: B 301 LYS cc_start: 0.7836 (ttpt) cc_final: 0.7153 (ttpt) REVERT: B 466 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: B 548 TYR cc_start: 0.8786 (m-80) cc_final: 0.7717 (t80) REVERT: B 553 ARG cc_start: 0.8048 (mtp-110) cc_final: 0.7629 (mtm-85) REVERT: B 555 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8084 (mm-30) REVERT: B 562 ASP cc_start: 0.8520 (m-30) cc_final: 0.8285 (m-30) REVERT: C 30 LYS cc_start: 0.7913 (mttp) cc_final: 0.7387 (mtpp) REVERT: C 64 LYS cc_start: 0.8748 (mtpp) cc_final: 0.7910 (mttp) REVERT: C 68 LYS cc_start: 0.8311 (ptmt) cc_final: 0.7771 (ptmm) REVERT: C 82 LYS cc_start: 0.8176 (mttp) cc_final: 0.7780 (mtpt) REVERT: C 119 ASN cc_start: 0.8363 (m-40) cc_final: 0.7892 (m-40) REVERT: C 141 ARG cc_start: 0.8506 (mtt-85) cc_final: 0.8059 (mtp85) REVERT: C 157 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8224 (mtmt) REVERT: C 205 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8168 (t) REVERT: C 258 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: C 394 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8027 (tt) REVERT: C 408 LYS cc_start: 0.8263 (ptmt) cc_final: 0.7940 (ptpp) REVERT: C 427 GLU cc_start: 0.7366 (mp0) cc_final: 0.6989 (mt-10) REVERT: D 65 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: D 129 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7643 (mp) REVERT: D 206 ASP cc_start: 0.8210 (m-30) cc_final: 0.7697 (m-30) REVERT: D 258 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7644 (mm-30) REVERT: D 328 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7841 (mttp) REVERT: D 344 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7000 (mtt180) REVERT: D 427 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6982 (mt-10) REVERT: D 473 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7643 (mm-30) REVERT: D 482 PHE cc_start: 0.8310 (m-80) cc_final: 0.8023 (m-80) REVERT: D 490 PRO cc_start: 0.7379 (Cg_exo) cc_final: 0.7123 (Cg_endo) REVERT: D 545 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: D 555 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7714 (mm-30) REVERT: D 563 LYS cc_start: 0.8395 (mmtp) cc_final: 0.8073 (mmtm) REVERT: E 7 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8274 (tp) REVERT: E 20 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8316 (mttp) REVERT: E 64 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7487 (mttp) REVERT: E 171 GLU cc_start: 0.7425 (pt0) cc_final: 0.6758 (mt-10) REVERT: E 256 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8131 (p) REVERT: E 263 HIS cc_start: 0.7651 (p-80) cc_final: 0.6489 (m90) REVERT: E 312 LYS cc_start: 0.7686 (mmtp) cc_final: 0.7214 (mmpt) REVERT: E 386 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: E 401 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7915 (mm-30) REVERT: E 411 ARG cc_start: 0.6793 (mtp180) cc_final: 0.6465 (mmm160) REVERT: E 430 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8039 (mtmt) REVERT: E 436 ASP cc_start: 0.8203 (t0) cc_final: 0.7935 (t0) REVERT: E 516 GLU cc_start: 0.7327 (pm20) cc_final: 0.7066 (mp0) REVERT: E 562 ASP cc_start: 0.8380 (m-30) cc_final: 0.8151 (m-30) REVERT: F 64 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8069 (mttp) REVERT: F 104 LYS cc_start: 0.7790 (mttt) cc_final: 0.7237 (mmtp) REVERT: F 115 SER cc_start: 0.8620 (t) cc_final: 0.8410 (p) REVERT: F 328 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7177 (ptpt) REVERT: F 370 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8299 (tttm) REVERT: F 386 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: F 436 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7478 (t0) REVERT: F 441 ARG cc_start: 0.7863 (ptt-90) cc_final: 0.7585 (ptt-90) REVERT: G 176 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6145 (mm-30) REVERT: G 198 ARG cc_start: 0.3960 (OUTLIER) cc_final: 0.3588 (tpm170) REVERT: G 231 LYS cc_start: 0.7707 (tptt) cc_final: 0.7378 (tptp) REVERT: G 345 ASP cc_start: 0.7806 (m-30) cc_final: 0.7483 (m-30) REVERT: G 359 ARG cc_start: 0.7922 (ttt90) cc_final: 0.7539 (tmt-80) REVERT: H 194 LYS cc_start: 0.4969 (OUTLIER) cc_final: 0.4578 (pmmt) REVERT: H 226 LYS cc_start: 0.8093 (mmmm) cc_final: 0.7418 (tmmm) REVERT: H 231 LYS cc_start: 0.7655 (mmmm) cc_final: 0.7316 (ttmt) REVERT: H 238 ARG cc_start: 0.7724 (ttp-110) cc_final: 0.7454 (mmm-85) REVERT: H 254 PHE cc_start: 0.8344 (t80) cc_final: 0.8126 (t80) REVERT: H 327 LYS cc_start: 0.7855 (ttpp) cc_final: 0.7644 (ttpp) REVERT: H 383 GLN cc_start: 0.8521 (tt0) cc_final: 0.8247 (tt0) REVERT: I 153 PHE cc_start: 0.2346 (OUTLIER) cc_final: 0.1701 (t80) REVERT: I 214 LEU cc_start: 0.7864 (mm) cc_final: 0.7602 (mt) REVERT: I 301 GLU cc_start: 0.8163 (tp30) cc_final: 0.7888 (tm-30) REVERT: I 344 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8248 (m110) REVERT: I 377 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7359 (pp) REVERT: I 389 ASP cc_start: 0.7075 (m-30) cc_final: 0.6500 (m-30) REVERT: J 314 THR cc_start: 0.9166 (p) cc_final: 0.8755 (t) REVERT: L 153 PHE cc_start: 0.3652 (OUTLIER) cc_final: 0.3341 (t80) REVERT: L 156 GLN cc_start: 0.5398 (OUTLIER) cc_final: 0.4061 (pm20) REVERT: L 253 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: L 328 MET cc_start: 0.8793 (mmp) cc_final: 0.8414 (mmp) REVERT: L 331 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7713 (pt0) REVERT: L 376 GLN cc_start: 0.8377 (pm20) cc_final: 0.8174 (pm20) REVERT: M 233 LYS cc_start: 0.7466 (tttt) cc_final: 0.6551 (tptm) REVERT: M 280 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6869 (ptm160) REVERT: M 299 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8345 (tp) REVERT: M 337 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8157 (mm-30) REVERT: N 279 LYS cc_start: 0.8149 (pptt) cc_final: 0.7569 (mppt) REVERT: N 314 THR cc_start: 0.8631 (p) cc_final: 0.8256 (t) REVERT: N 376 GLN cc_start: 0.8526 (pm20) cc_final: 0.8276 (pm20) REVERT: N 392 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: O 227 GLU cc_start: 0.6132 (OUTLIER) cc_final: 0.5834 (pp20) REVERT: O 301 GLU cc_start: 0.8162 (tp30) cc_final: 0.7659 (tp30) REVERT: O 314 THR cc_start: 0.8862 (p) cc_final: 0.8423 (t) REVERT: O 369 ASN cc_start: 0.8090 (m110) cc_final: 0.7603 (m-40) REVERT: P 327 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7896 (ttmt) REVERT: Q 237 ILE cc_start: 0.4601 (OUTLIER) cc_final: 0.4285 (mm) REVERT: Q 302 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8438 (tp) REVERT: Q 386 ASP cc_start: 0.7894 (m-30) cc_final: 0.7591 (p0) REVERT: Q 392 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: R 228 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.5526 (p90) REVERT: R 351 GLU cc_start: 0.7733 (tt0) cc_final: 0.7361 (tt0) REVERT: R 355 SER cc_start: 0.8762 (m) cc_final: 0.8423 (p) REVERT: R 392 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7372 (mt-10) outliers start: 222 outliers final: 121 residues processed: 759 average time/residue: 1.3041 time to fit residues: 1237.4505 Evaluate side-chains 724 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 554 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 467 ARG Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 555 GLU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 537 CYS Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 436 ASP Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 567 GLN Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 198 ARG Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain H residue 194 LYS Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain I residue 153 PHE Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 344 ASN Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 281 THR Chi-restraints excluded: chain J residue 325 THR Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain K residue 153 PHE Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 281 THR Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 153 PHE Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 253 GLU Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 280 ARG Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 360 LYS Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 392 GLU Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 375 SER Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 244 SER Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 392 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 395 optimal weight: 2.9990 chunk 431 optimal weight: 7.9990 chunk 285 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 411 optimal weight: 20.0000 chunk 170 optimal weight: 0.2980 chunk 405 optimal weight: 2.9990 chunk 582 optimal weight: 8.9990 chunk 266 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN C 282 ASN D 144 ASN D 478 GLN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 47 ASN E 240 GLN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 379 GLN I 216 ASN I 344 ASN ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 379 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 364 GLN Q 242 ASN Q 273 ASN ** Q 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 379 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.146939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107943 restraints weight = 58581.574| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.01 r_work: 0.3065 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 50071 Z= 0.232 Angle : 0.510 7.849 67707 Z= 0.268 Chirality : 0.044 0.219 7377 Planarity : 0.004 0.058 8640 Dihedral : 9.151 174.767 6748 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.76 % Allowed : 26.98 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.11), residues: 5849 helix: 0.60 (0.11), residues: 2303 sheet: -0.61 (0.16), residues: 917 loop : -0.36 (0.12), residues: 2629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 274 HIS 0.006 0.001 HIS J 177 PHE 0.024 0.001 PHE I 184 TYR 0.019 0.001 TYR H 180 ARG 0.010 0.000 ARG H 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 576 time to evaluate : 4.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: A 74 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8157 (mm-30) REVERT: A 118 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8484 (tp) REVERT: A 231 ASP cc_start: 0.6715 (t70) cc_final: 0.6341 (t70) REVERT: A 309 ARG cc_start: 0.8408 (ptm160) cc_final: 0.7849 (ptm160) REVERT: A 312 LYS cc_start: 0.7145 (mtmt) cc_final: 0.6414 (pttt) REVERT: A 335 ARG cc_start: 0.7077 (mtm-85) cc_final: 0.6819 (mtt-85) REVERT: A 377 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8468 (mm) REVERT: A 445 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7118 (tt0) REVERT: A 466 GLN cc_start: 0.8552 (pm20) cc_final: 0.8203 (pm20) REVERT: A 467 ARG cc_start: 0.7786 (ttp-110) cc_final: 0.7487 (mtp180) REVERT: B 28 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: B 48 GLN cc_start: 0.8873 (mt0) cc_final: 0.8654 (mt0) REVERT: B 64 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7552 (mttp) REVERT: B 74 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8127 (mp0) REVERT: B 88 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7868 (mtp85) REVERT: B 221 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7653 (tt0) REVERT: B 301 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7153 (ttpt) REVERT: B 466 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: B 548 TYR cc_start: 0.8784 (m-80) cc_final: 0.7735 (t80) REVERT: B 553 ARG cc_start: 0.8033 (mtp-110) cc_final: 0.7632 (mtm-85) REVERT: B 555 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8070 (mm-30) REVERT: B 562 ASP cc_start: 0.8479 (m-30) cc_final: 0.8232 (m-30) REVERT: C 30 LYS cc_start: 0.7920 (mttp) cc_final: 0.7415 (mtpp) REVERT: C 64 LYS cc_start: 0.8708 (mtpp) cc_final: 0.7914 (mttp) REVERT: C 82 LYS cc_start: 0.8153 (mttp) cc_final: 0.7754 (mtpt) REVERT: C 119 ASN cc_start: 0.8368 (m-40) cc_final: 0.7633 (t0) REVERT: C 141 ARG cc_start: 0.8509 (mtt-85) cc_final: 0.8064 (mtp85) REVERT: C 157 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8210 (mtmt) REVERT: C 205 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8171 (t) REVERT: C 258 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: C 394 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8088 (tt) REVERT: C 408 LYS cc_start: 0.8252 (ptmt) cc_final: 0.7906 (ptmt) REVERT: C 427 GLU cc_start: 0.7426 (mp0) cc_final: 0.7023 (mm-30) REVERT: C 547 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8295 (mmtp) REVERT: D 65 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: D 129 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7595 (mp) REVERT: D 206 ASP cc_start: 0.8173 (m-30) cc_final: 0.7672 (m-30) REVERT: D 258 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7586 (mm-30) REVERT: D 328 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7811 (mttp) REVERT: D 344 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.6944 (mtt180) REVERT: D 473 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7638 (mm-30) REVERT: D 482 PHE cc_start: 0.8412 (m-80) cc_final: 0.8149 (m-80) REVERT: D 490 PRO cc_start: 0.7369 (Cg_exo) cc_final: 0.7119 (Cg_endo) REVERT: D 545 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: D 555 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7704 (mm-30) REVERT: D 563 LYS cc_start: 0.8355 (mmtp) cc_final: 0.8055 (mmtm) REVERT: E 7 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8256 (tp) REVERT: E 20 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8306 (mttp) REVERT: E 64 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7481 (mttp) REVERT: E 106 ASP cc_start: 0.7741 (p0) cc_final: 0.7483 (t0) REVERT: E 171 GLU cc_start: 0.7475 (pt0) cc_final: 0.6832 (mt-10) REVERT: E 256 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8118 (p) REVERT: E 263 HIS cc_start: 0.7631 (p-80) cc_final: 0.6482 (m90) REVERT: E 312 LYS cc_start: 0.7682 (mmtp) cc_final: 0.7204 (mmpt) REVERT: E 386 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: E 401 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7765 (mm-30) REVERT: E 411 ARG cc_start: 0.6766 (mtp180) cc_final: 0.6449 (mmm160) REVERT: E 430 LYS cc_start: 0.8355 (mtpt) cc_final: 0.8001 (mtmt) REVERT: E 436 ASP cc_start: 0.8151 (t0) cc_final: 0.7904 (t0) REVERT: E 466 GLN cc_start: 0.8020 (tt0) cc_final: 0.7597 (pt0) REVERT: E 516 GLU cc_start: 0.7307 (pm20) cc_final: 0.7038 (mp0) REVERT: E 562 ASP cc_start: 0.8374 (m-30) cc_final: 0.8114 (m-30) REVERT: F 64 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8057 (mttp) REVERT: F 104 LYS cc_start: 0.7771 (mttt) cc_final: 0.7215 (mmtp) REVERT: F 328 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7147 (ptpt) REVERT: F 386 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: F 436 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7482 (t0) REVERT: F 441 ARG cc_start: 0.7850 (ptt-90) cc_final: 0.7546 (ptt-90) REVERT: G 179 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.5383 (mm) REVERT: G 345 ASP cc_start: 0.7807 (m-30) cc_final: 0.7490 (m-30) REVERT: G 359 ARG cc_start: 0.7924 (ttt90) cc_final: 0.7550 (tmt-80) REVERT: H 194 LYS cc_start: 0.4928 (OUTLIER) cc_final: 0.4485 (pmmt) REVERT: H 226 LYS cc_start: 0.8106 (mmmm) cc_final: 0.7418 (tmmm) REVERT: H 231 LYS cc_start: 0.7671 (mmmm) cc_final: 0.7332 (ttmt) REVERT: H 238 ARG cc_start: 0.7632 (ttp-110) cc_final: 0.7182 (mtm180) REVERT: H 327 LYS cc_start: 0.7824 (ttpp) cc_final: 0.7615 (ttpp) REVERT: H 383 GLN cc_start: 0.8523 (tt0) cc_final: 0.8185 (tt0) REVERT: I 153 PHE cc_start: 0.2374 (OUTLIER) cc_final: 0.1737 (t80) REVERT: I 214 LEU cc_start: 0.7830 (mm) cc_final: 0.7574 (mt) REVERT: I 301 GLU cc_start: 0.8101 (tp30) cc_final: 0.7832 (tm-30) REVERT: I 344 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8205 (m110) REVERT: I 377 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7370 (pp) REVERT: I 389 ASP cc_start: 0.7065 (m-30) cc_final: 0.6482 (m-30) REVERT: J 314 THR cc_start: 0.9176 (p) cc_final: 0.8761 (t) REVERT: L 153 PHE cc_start: 0.3921 (OUTLIER) cc_final: 0.3613 (t80) REVERT: L 156 GLN cc_start: 0.5358 (OUTLIER) cc_final: 0.4013 (pm20) REVERT: L 253 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: L 331 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7783 (pt0) REVERT: M 233 LYS cc_start: 0.7452 (tttt) cc_final: 0.6558 (tptm) REVERT: M 280 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6887 (ptm160) REVERT: M 299 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8344 (tp) REVERT: M 337 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8156 (mm-30) REVERT: M 379 GLN cc_start: 0.8599 (pm20) cc_final: 0.8392 (pm20) REVERT: N 279 LYS cc_start: 0.8154 (pptt) cc_final: 0.7573 (mppt) REVERT: N 314 THR cc_start: 0.8624 (p) cc_final: 0.8235 (t) REVERT: N 376 GLN cc_start: 0.8545 (pm20) cc_final: 0.8301 (pm20) REVERT: N 392 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: O 227 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.5925 (pp20) REVERT: O 301 GLU cc_start: 0.8104 (tp30) cc_final: 0.7604 (tp30) REVERT: O 314 THR cc_start: 0.8862 (p) cc_final: 0.8424 (t) REVERT: O 369 ASN cc_start: 0.8045 (m110) cc_final: 0.7590 (m-40) REVERT: P 327 LYS cc_start: 0.8262 (ttpp) cc_final: 0.7974 (ttmt) REVERT: Q 302 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8413 (tp) REVERT: Q 386 ASP cc_start: 0.7948 (m-30) cc_final: 0.7641 (p0) REVERT: Q 392 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: R 228 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.5525 (p90) REVERT: R 351 GLU cc_start: 0.7713 (tt0) cc_final: 0.7328 (tt0) REVERT: R 355 SER cc_start: 0.8767 (m) cc_final: 0.8433 (p) REVERT: R 392 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7288 (mt-10) outliers start: 206 outliers final: 128 residues processed: 739 average time/residue: 1.2827 time to fit residues: 1186.6140 Evaluate side-chains 718 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 543 time to evaluate : 4.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 547 LYS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 467 ARG Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 555 GLU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 537 CYS Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 436 ASP Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 567 GLN Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 379 GLN Chi-restraints excluded: chain H residue 194 LYS Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain I residue 153 PHE Chi-restraints excluded: chain I residue 216 ASN Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 344 ASN Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 281 THR Chi-restraints excluded: chain J residue 325 THR Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain K residue 153 PHE Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 281 THR Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 153 PHE Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 253 GLU Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 373 ILE Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 280 ARG Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 360 LYS Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 392 GLU Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 375 SER Chi-restraints excluded: chain Q residue 244 SER Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 314 THR Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain R residue 392 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 216 optimal weight: 9.9990 chunk 267 optimal weight: 0.0010 chunk 89 optimal weight: 8.9990 chunk 398 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 579 optimal weight: 8.9990 chunk 328 optimal weight: 1.9990 chunk 460 optimal weight: 10.0000 chunk 458 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 239 optimal weight: 6.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN C 5 ASN C 282 ASN D 144 ASN D 414 ASN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN E 47 ASN E 240 GLN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 369 ASN H 379 GLN I 216 ASN I 344 ASN ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 GLN ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 364 GLN Q 242 ASN ** Q 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 379 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106089 restraints weight = 58849.334| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.00 r_work: 0.3031 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 50071 Z= 0.350 Angle : 0.563 8.369 67707 Z= 0.293 Chirality : 0.046 0.248 7377 Planarity : 0.004 0.058 8640 Dihedral : 9.312 175.116 6748 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.69 % Allowed : 27.18 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.11), residues: 5849 helix: 0.51 (0.11), residues: 2291 sheet: -0.60 (0.16), residues: 938 loop : -0.41 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 218 HIS 0.007 0.001 HIS J 177 PHE 0.021 0.002 PHE I 184 TYR 0.021 0.002 TYR H 180 ARG 0.010 0.001 ARG H 230 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 558 time to evaluate : 4.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: A 74 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8238 (mm-30) REVERT: A 118 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8498 (tp) REVERT: A 119 ASN cc_start: 0.8352 (m-40) cc_final: 0.7526 (p0) REVERT: A 231 ASP cc_start: 0.6701 (t70) cc_final: 0.6358 (t70) REVERT: A 284 ARG cc_start: 0.6735 (mtp85) cc_final: 0.6365 (mtp85) REVERT: A 309 ARG cc_start: 0.8345 (ptm160) cc_final: 0.7847 (ptm160) REVERT: A 335 ARG cc_start: 0.7109 (mtm-85) cc_final: 0.6844 (mtt-85) REVERT: A 377 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8549 (mm) REVERT: A 445 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: A 466 GLN cc_start: 0.8556 (pm20) cc_final: 0.8308 (pm20) REVERT: A 467 ARG cc_start: 0.7820 (ttp-110) cc_final: 0.7504 (mtp180) REVERT: B 28 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: B 64 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7564 (mttp) REVERT: B 74 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8193 (mp0) REVERT: B 88 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8580 (ttp-110) REVERT: B 221 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7704 (tt0) REVERT: B 301 LYS cc_start: 0.7800 (ttpt) cc_final: 0.7135 (ttpt) REVERT: B 337 GLN cc_start: 0.8059 (mt0) cc_final: 0.7818 (mt0) REVERT: B 466 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: B 548 TYR cc_start: 0.8796 (m-80) cc_final: 0.7665 (t80) REVERT: B 553 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7624 (mtm-85) REVERT: B 555 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: B 562 ASP cc_start: 0.8571 (m-30) cc_final: 0.8341 (m-30) REVERT: C 30 LYS cc_start: 0.7952 (mttp) cc_final: 0.7454 (mtpp) REVERT: C 64 LYS cc_start: 0.8735 (mtpp) cc_final: 0.7902 (mttp) REVERT: C 68 LYS cc_start: 0.8305 (ptmt) cc_final: 0.7792 (ptmm) REVERT: C 82 LYS cc_start: 0.8172 (mttp) cc_final: 0.7766 (mtpt) REVERT: C 119 ASN cc_start: 0.8350 (m-40) cc_final: 0.7813 (m-40) REVERT: C 141 ARG cc_start: 0.8531 (mtt-85) cc_final: 0.8072 (mtp85) REVERT: C 157 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8330 (mtmt) REVERT: C 205 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8241 (t) REVERT: C 258 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: C 394 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8058 (tt) REVERT: C 408 LYS cc_start: 0.8327 (ptmt) cc_final: 0.7982 (ptpp) REVERT: C 427 GLU cc_start: 0.7495 (mp0) cc_final: 0.7109 (mm-30) REVERT: C 547 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8313 (mmtp) REVERT: D 65 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: D 129 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7744 (mp) REVERT: D 206 ASP cc_start: 0.8199 (m-30) cc_final: 0.7735 (m-30) REVERT: D 258 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7654 (mm-30) REVERT: D 328 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7857 (mttp) REVERT: D 344 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6967 (mtt180) REVERT: D 473 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: D 482 PHE cc_start: 0.8477 (m-80) cc_final: 0.8240 (m-80) REVERT: D 490 PRO cc_start: 0.7412 (Cg_exo) cc_final: 0.7151 (Cg_endo) REVERT: D 545 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: D 555 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7678 (mm-30) REVERT: D 563 LYS cc_start: 0.8381 (mmtp) cc_final: 0.8082 (mmtm) REVERT: E 7 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8281 (tp) REVERT: E 20 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8315 (mttp) REVERT: E 64 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7512 (mttp) REVERT: E 106 ASP cc_start: 0.7764 (p0) cc_final: 0.7509 (t0) REVERT: E 171 GLU cc_start: 0.7575 (pt0) cc_final: 0.6955 (mt-10) REVERT: E 256 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8117 (p) REVERT: E 263 HIS cc_start: 0.7665 (p-80) cc_final: 0.6481 (m90) REVERT: E 312 LYS cc_start: 0.7663 (mmtp) cc_final: 0.7180 (mmpt) REVERT: E 386 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: E 401 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7888 (mm-30) REVERT: E 411 ARG cc_start: 0.6771 (mtp180) cc_final: 0.6457 (mmm160) REVERT: E 430 LYS cc_start: 0.8362 (mtpt) cc_final: 0.8002 (mtmt) REVERT: E 436 ASP cc_start: 0.8238 (t0) cc_final: 0.7992 (t0) REVERT: E 466 GLN cc_start: 0.8111 (tt0) cc_final: 0.7674 (pt0) REVERT: E 516 GLU cc_start: 0.7318 (pm20) cc_final: 0.7041 (mp0) REVERT: E 562 ASP cc_start: 0.8386 (m-30) cc_final: 0.8174 (m-30) REVERT: F 64 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8122 (mttp) REVERT: F 104 LYS cc_start: 0.7791 (mttt) cc_final: 0.7230 (mmtp) REVERT: F 328 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7250 (ptpt) REVERT: F 386 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: F 436 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7554 (t0) REVERT: F 441 ARG cc_start: 0.7819 (ptt-90) cc_final: 0.7494 (ptt-90) REVERT: F 518 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8398 (mt-10) REVERT: G 198 ARG cc_start: 0.3951 (OUTLIER) cc_final: 0.3572 (tpm170) REVERT: G 345 ASP cc_start: 0.7826 (m-30) cc_final: 0.7521 (m-30) REVERT: G 359 ARG cc_start: 0.7946 (ttt90) cc_final: 0.7544 (tmt-80) REVERT: H 194 LYS cc_start: 0.4889 (OUTLIER) cc_final: 0.4546 (pmmt) REVERT: H 226 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7461 (tmmm) REVERT: H 231 LYS cc_start: 0.7628 (mmmm) cc_final: 0.7280 (ttmt) REVERT: H 238 ARG cc_start: 0.7675 (ttp-110) cc_final: 0.7398 (mmm-85) REVERT: H 327 LYS cc_start: 0.7883 (ttpp) cc_final: 0.7667 (ttpp) REVERT: H 383 GLN cc_start: 0.8643 (tt0) cc_final: 0.8330 (tt0) REVERT: I 153 PHE cc_start: 0.2316 (OUTLIER) cc_final: 0.1646 (t80) REVERT: I 214 LEU cc_start: 0.7842 (mm) cc_final: 0.7560 (mt) REVERT: I 301 GLU cc_start: 0.8160 (tp30) cc_final: 0.7898 (tm-30) REVERT: I 377 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7353 (pp) REVERT: I 389 ASP cc_start: 0.7094 (m-30) cc_final: 0.6504 (m-30) REVERT: L 153 PHE cc_start: 0.4040 (OUTLIER) cc_final: 0.3712 (t80) REVERT: L 156 GLN cc_start: 0.5474 (OUTLIER) cc_final: 0.4207 (pm20) REVERT: L 184 PHE cc_start: 0.5886 (t80) cc_final: 0.5643 (t80) REVERT: L 253 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: L 331 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7778 (pt0) REVERT: M 233 LYS cc_start: 0.7400 (tttt) cc_final: 0.6474 (tptm) REVERT: M 280 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6924 (ptm160) REVERT: M 299 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8351 (tp) REVERT: M 337 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8153 (mm-30) REVERT: N 279 LYS cc_start: 0.8148 (pptt) cc_final: 0.7562 (mppt) REVERT: N 314 THR cc_start: 0.8691 (p) cc_final: 0.8275 (t) REVERT: N 331 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7625 (mt-10) REVERT: N 376 GLN cc_start: 0.8556 (pm20) cc_final: 0.8297 (pm20) REVERT: N 392 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: O 227 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.6073 (pp20) REVERT: O 301 GLU cc_start: 0.8138 (tp30) cc_final: 0.7602 (tp30) REVERT: O 314 THR cc_start: 0.8866 (p) cc_final: 0.8423 (t) REVERT: O 369 ASN cc_start: 0.8032 (m110) cc_final: 0.7574 (m-40) REVERT: P 327 LYS cc_start: 0.8290 (ttpp) cc_final: 0.7993 (ttmt) REVERT: P 368 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8088 (tt0) REVERT: Q 237 ILE cc_start: 0.4511 (OUTLIER) cc_final: 0.4158 (mm) REVERT: Q 302 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8453 (tp) REVERT: Q 386 ASP cc_start: 0.7845 (m-30) cc_final: 0.7598 (p0) REVERT: Q 392 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: R 228 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.5595 (p90) REVERT: R 351 GLU cc_start: 0.7727 (tt0) cc_final: 0.7363 (tt0) REVERT: R 355 SER cc_start: 0.8771 (m) cc_final: 0.8406 (p) REVERT: R 392 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7369 (mt-10) outliers start: 202 outliers final: 132 residues processed: 719 average time/residue: 1.2991 time to fit residues: 1167.4983 Evaluate side-chains 724 residues out of total 5475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 545 time to evaluate : 4.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 547 LYS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 467 ARG Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 555 GLU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 537 CYS Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 436 ASP Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 567 GLN Chi-restraints excluded: chain G residue 198 ARG Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 379 GLN Chi-restraints excluded: chain H residue 194 LYS Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain I residue 153 PHE Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 281 THR Chi-restraints excluded: chain J residue 325 THR Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain K residue 153 PHE Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 281 THR Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 153 PHE Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 253 GLU Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 373 ILE Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 280 ARG Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 392 GLU Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 375 SER Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 244 SER Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 314 THR Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain R residue 392 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 512 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 573 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 496 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 437 optimal weight: 0.8980 chunk 362 optimal weight: 20.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN C 282 ASN D 144 ASN D 414 ASN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN E 47 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 379 GLN I 216 ASN I 344 ASN ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 GLN ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 379 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 364 GLN Q 242 ASN ** Q 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 379 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.146601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107831 restraints weight = 58533.193| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.98 r_work: 0.3069 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 50071 Z= 0.246 Angle : 0.521 8.572 67707 Z= 0.273 Chirality : 0.044 0.225 7377 Planarity : 0.004 0.058 8640 Dihedral : 9.186 174.218 6748 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.73 % Allowed : 27.16 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.11), residues: 5849 helix: 0.58 (0.11), residues: 2302 sheet: -0.60 (0.16), residues: 923 loop : -0.39 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 274 HIS 0.006 0.001 HIS J 177 PHE 0.024 0.001 PHE I 184 TYR 0.024 0.001 TYR H 180 ARG 0.008 0.000 ARG J 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35887.39 seconds wall clock time: 613 minutes 19.30 seconds (36799.30 seconds total)