Starting phenix.real_space_refine on Tue Sep 24 00:24:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xay_38207/09_2024/8xay_38207.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xay_38207/09_2024/8xay_38207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xay_38207/09_2024/8xay_38207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xay_38207/09_2024/8xay_38207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xay_38207/09_2024/8xay_38207.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xay_38207/09_2024/8xay_38207.cif" } resolution = 2.81 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= 0.068 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 42 5.49 5 Mg 6 5.21 5 S 88 5.16 5 C 31189 2.51 5 N 8164 2.21 5 O 9498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 48987 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: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "T" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 265 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 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, 'AGS': 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, 'AGS': 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, 'AGS': 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: 21.49, per 1000 atoms: 0.44 Number of scatterers: 48987 At special positions: 0 Unit cell: (189.05, 177.65, 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 88 16.00 P 42 15.00 Mg 6 11.99 O 9498 8.00 N 8164 7.00 C 31189 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.01 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: 251 helices and 30 sheets defined 44.2% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.79 Creating SS restraints... Processing helix chain 'A' and resid 28 through 36 removed outlier: 4.322A pdb=" N ALA A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.878A pdb=" N TYR A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.792A 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: 3.627A pdb=" N PHE A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 231 through 249 removed outlier: 3.982A pdb=" N LYS A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 306 through 311 removed outlier: 3.776A pdb=" N ARG A 309 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.671A pdb=" N ASP A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.501A 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 366 Processing helix chain 'A' and resid 384 through 414 removed outlier: 4.579A pdb=" N SER A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 409 " --> pdb=" O HIS A 405 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.769A pdb=" N TYR A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 458 removed outlier: 5.431A pdb=" N ARG A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 489 through 500 Processing helix chain 'A' and resid 506 through 511 Processing helix chain 'A' and resid 547 through 554 removed outlier: 3.792A pdb=" N LYS A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'B' and resid 28 through 36 removed outlier: 4.220A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 114 removed outlier: 3.827A pdb=" N TYR B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.836A pdb=" N PHE B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 3.584A 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 217 through 225 removed outlier: 3.798A pdb=" N PHE B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 249 removed outlier: 3.828A pdb=" N VAL B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 238 " --> pdb=" O GLN B 234 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 281 Processing helix chain 'B' and resid 306 through 312 removed outlier: 3.631A pdb=" N LYS B 312 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.622A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 427 through 432 removed outlier: 4.240A pdb=" N TYR B 431 " --> pdb=" O GLU B 427 " (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: 3.628A pdb=" N ALA B 446 " --> pdb=" O THR B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 4.146A pdb=" N TYR B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) 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: 3.702A pdb=" N ILE B 507 " --> pdb=" O VAL B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 571 removed outlier: 3.616A pdb=" N GLN B 567 " --> pdb=" O LYS B 563 " (cutoff:3.500A) removed outlier: 3.835A 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: 4.271A pdb=" N TYR C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 145 removed outlier: 3.579A pdb=" N PHE C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 4.273A 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: 3.973A pdb=" N ALA C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 231 through 249 Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.529A pdb=" N GLU C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.816A pdb=" N LYS C 312 " --> pdb=" O ARG C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 341 removed outlier: 3.632A pdb=" N LYS C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.873A pdb=" N SER C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 366 Processing helix chain 'C' and resid 384 through 413 removed outlier: 3.603A pdb=" N ILE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 440 through 454 Processing helix chain 'C' and resid 472 through 477 removed outlier: 3.582A pdb=" N PHE C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 500 removed outlier: 3.634A pdb=" N LEU C 499 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 500 " --> pdb=" O VAL C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 511 removed outlier: 3.615A pdb=" N LEU C 510 " --> pdb=" O ILE C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 553 Processing helix chain 'C' and resid 560 through 571 removed outlier: 3.573A pdb=" N ILE C 564 " --> pdb=" O GLU C 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 35 removed outlier: 4.146A pdb=" N ALA D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 116 removed outlier: 4.259A pdb=" N TYR D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE D 116 " --> pdb=" O TYR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.611A pdb=" N PHE D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 4.164A 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 192 through 197 removed outlier: 4.155A pdb=" N ALA D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 215 Processing helix chain 'D' and resid 216 through 225 removed outlier: 3.619A pdb=" N GLU D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 222 " --> pdb=" O ASP D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 250 Processing helix chain 'D' and resid 253 through 259 removed outlier: 3.922A 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 312 removed outlier: 3.824A pdb=" N LYS D 312 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 341 Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 351 through 356 removed outlier: 3.925A pdb=" N SER D 355 " --> pdb=" O GLU D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 366 Processing helix chain 'D' and resid 384 through 413 removed outlier: 4.045A pdb=" N ILE D 390 " --> pdb=" O GLU D 386 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 454 removed outlier: 3.804A pdb=" N ALA D 446 " --> pdb=" O THR D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 478 removed outlier: 3.570A pdb=" N GLN D 478 " --> pdb=" O THR D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 500 removed outlier: 3.652A pdb=" N TYR D 495 " --> pdb=" O ASP D 491 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 499 " --> pdb=" O TYR D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 511 Processing helix chain 'D' and resid 547 through 554 removed outlier: 3.821A pdb=" N LYS D 554 " --> pdb=" O ASP D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 571 removed outlier: 4.023A pdb=" N ILE D 564 " --> pdb=" O GLU D 560 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN D 567 " --> pdb=" O LYS D 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 35 removed outlier: 4.313A pdb=" N ALA E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.919A pdb=" N TYR E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 145 removed outlier: 3.799A 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: 4.057A pdb=" N ALA E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 215 removed outlier: 3.522A pdb=" N LEU E 214 " --> pdb=" O PRO E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 225 Processing helix chain 'E' and resid 231 through 249 Processing helix chain 'E' and resid 253 through 259 removed outlier: 3.935A pdb=" N ILE E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 282 Processing helix chain 'E' and resid 306 through 312 Processing helix chain 'E' and resid 329 through 342 removed outlier: 3.632A pdb=" N LYS E 339 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE E 340 " --> pdb=" O LEU E 336 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP E 342 " --> pdb=" O SER E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 351 through 356 removed outlier: 3.972A pdb=" N SER E 355 " --> pdb=" O GLU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 366 Processing helix chain 'E' and resid 384 through 386 No H-bonds generated for 'chain 'E' and resid 384 through 386' Processing helix chain 'E' and resid 387 through 413 removed outlier: 3.615A pdb=" N LYS E 412 " --> pdb=" O LYS E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 432 removed outlier: 4.279A 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 454 Processing helix chain 'E' and resid 455 through 457 No H-bonds generated for 'chain 'E' and resid 455 through 457' Processing helix chain 'E' and resid 467 through 471 Processing helix chain 'E' and resid 472 through 479 removed outlier: 3.746A pdb=" N GLN E 478 " --> pdb=" O THR E 474 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS E 479 " --> pdb=" O ILE E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 500 Processing helix chain 'E' and resid 547 through 554 removed outlier: 3.792A pdb=" N LYS E 554 " --> pdb=" O ASP E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 571 removed outlier: 4.536A pdb=" N ASP E 562 " --> pdb=" O ASP E 558 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS E 563 " --> pdb=" O SER E 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 35 removed outlier: 4.301A pdb=" N ALA F 32 " --> pdb=" O GLU F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 114 removed outlier: 3.889A pdb=" N TYR F 112 " --> pdb=" O ILE F 108 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.935A pdb=" N PHE F 143 " --> pdb=" O GLY F 139 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS F 145 " --> pdb=" O ARG F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 170 Processing helix chain 'F' and resid 192 through 197 removed outlier: 4.274A pdb=" N ALA F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 215 Processing helix chain 'F' and resid 216 through 225 Processing helix chain 'F' and resid 231 through 249 removed outlier: 3.924A pdb=" N VAL F 237 " --> pdb=" O ASN F 233 " (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 311 removed outlier: 4.039A pdb=" N HIS F 308 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG F 309 " --> pdb=" O ASN F 306 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE F 311 " --> pdb=" O HIS F 308 " (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: 3.791A pdb=" N LYS F 354 " --> pdb=" O GLY F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 367 removed outlier: 3.569A pdb=" N LEU F 362 " --> pdb=" O PHE F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 414 removed outlier: 3.556A pdb=" N LYS F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS F 408 " --> pdb=" O TYR F 404 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS F 412 " --> pdb=" O LYS F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 432 removed outlier: 4.000A 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: 3.557A pdb=" N ARG F 498 " --> pdb=" O ASN F 494 " (cutoff:3.500A) removed outlier: 3.551A 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 512 through 514 No H-bonds generated for 'chain 'F' and resid 512 through 514' Processing helix chain 'F' and resid 547 through 554 removed outlier: 3.652A pdb=" N LYS F 554 " --> pdb=" O ASP F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 571 removed outlier: 4.264A pdb=" N ASP F 562 " --> pdb=" O ASP F 558 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS F 563 " --> pdb=" O SER F 559 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 169 removed outlier: 3.942A pdb=" N LYS G 158 " --> pdb=" O ASP G 154 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE G 164 " --> pdb=" O THR G 160 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN G 166 " --> pdb=" O GLN G 162 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE G 168 " --> pdb=" O ILE G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 178 removed outlier: 4.114A pdb=" N HIS G 177 " --> pdb=" O TYR G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 192 Processing helix chain 'G' and resid 201 through 209 removed outlier: 3.644A pdb=" N VAL G 205 " --> pdb=" O LYS G 201 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU G 206 " --> pdb=" O SER G 202 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER G 207 " --> pdb=" O ASP G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 222 Processing helix chain 'G' and resid 224 through 232 removed outlier: 4.191A pdb=" N ARG G 230 " --> pdb=" O LYS G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 237 removed outlier: 3.648A pdb=" N PHE G 236 " --> pdb=" O LEU G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 274 removed outlier: 3.598A pdb=" N ASP G 265 " --> pdb=" O LYS G 261 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N CYS G 266 " --> pdb=" O THR G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 309 removed outlier: 3.581A pdb=" N GLU G 309 " --> pdb=" O GLN G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 335 removed outlier: 3.607A pdb=" N SER G 334 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 355 removed outlier: 3.546A pdb=" N ASN G 354 " --> pdb=" O ASN G 350 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER G 355 " --> pdb=" O GLU G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 392 removed outlier: 4.251A pdb=" N LYS G 391 " --> pdb=" O PHE G 387 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU G 392 " --> pdb=" O ALA G 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 387 through 392' 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: 3.740A pdb=" N ILE H 161 " --> pdb=" O LYS H 157 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLN H 162 " --> pdb=" O LYS H 158 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE H 164 " --> pdb=" O THR H 160 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N HIS H 167 " --> pdb=" O ILE H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 177 removed outlier: 3.506A pdb=" N HIS H 177 " --> pdb=" O TYR H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 192 removed outlier: 4.032A 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: 3.844A 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 217 through 222 removed outlier: 3.543A pdb=" N TYR H 222 " --> pdb=" O TRP H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 234 removed outlier: 3.613A pdb=" N LEU H 229 " --> pdb=" O ARG H 225 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG H 230 " --> pdb=" O LYS H 226 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU H 234 " --> pdb=" O ARG H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 274 removed outlier: 3.728A pdb=" N CYS H 266 " --> pdb=" O THR H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 309 removed outlier: 3.605A pdb=" N LEU H 302 " --> pdb=" O ASN H 298 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN H 308 " --> pdb=" O ASN H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 335 removed outlier: 4.037A pdb=" N LEU H 329 " --> pdb=" O THR H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 354 removed outlier: 3.732A pdb=" N GLU H 351 " --> pdb=" O ASP H 347 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR H 352 " --> pdb=" O ASP H 348 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN H 354 " --> pdb=" O ASN H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 386 through 390 Processing helix chain 'I' and resid 152 through 169 removed outlier: 3.537A pdb=" N ILE I 161 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 178 removed outlier: 3.685A pdb=" N GLU I 176 " --> pdb=" O ASP I 172 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS I 177 " --> pdb=" O TYR I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 190 removed outlier: 3.628A 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 223 Processing helix chain 'I' and resid 224 through 234 Processing helix chain 'I' and resid 259 through 274 removed outlier: 3.744A pdb=" N VAL I 263 " --> pdb=" O ASP I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 309 removed outlier: 3.572A pdb=" N GLU I 309 " --> pdb=" O GLN I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 334 removed outlier: 3.580A pdb=" N ILE I 330 " --> pdb=" O PRO I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.570A pdb=" N PHE I 349 " --> pdb=" O ASP I 345 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN I 350 " --> pdb=" O ILE I 346 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU I 351 " --> pdb=" O ASP I 347 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN I 354 " --> pdb=" O ASN I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 392 removed outlier: 4.212A pdb=" N LYS I 391 " --> pdb=" O PHE I 387 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU I 392 " --> pdb=" O ALA I 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 387 through 392' Processing helix chain 'J' and resid 159 through 169 removed outlier: 3.984A pdb=" N ILE J 163 " --> pdb=" O GLU J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 177 removed outlier: 3.744A pdb=" N GLU J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 3.630A 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 178 through 193 removed outlier: 3.541A pdb=" N ASN J 182 " --> pdb=" O TYR J 178 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG J 185 " --> pdb=" O SER J 181 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN J 193 " --> pdb=" O ASP J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 209 removed outlier: 3.618A pdb=" N VAL J 205 " --> pdb=" O LYS J 201 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU J 206 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE J 208 " --> pdb=" O PHE J 204 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN J 209 " --> pdb=" O VAL J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 237 removed outlier: 4.034A pdb=" N GLU J 227 " --> pdb=" O GLU J 223 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS J 233 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU J 234 " --> pdb=" O ARG J 230 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER J 235 " --> pdb=" O LYS J 231 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE J 236 " --> pdb=" O LEU J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 274 removed outlier: 3.602A pdb=" N CYS J 266 " --> pdb=" O THR J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 309 Processing helix chain 'J' and resid 325 through 334 removed outlier: 4.264A pdb=" N LEU J 329 " --> pdb=" O THR J 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER J 334 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 345 through 356 removed outlier: 3.775A pdb=" N GLU J 351 " --> pdb=" O ASP J 347 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR J 352 " --> pdb=" O ASP J 348 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU J 353 " --> pdb=" O PHE J 349 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN J 354 " --> pdb=" O ASN J 350 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 392 removed outlier: 3.874A pdb=" N LYS J 391 " --> pdb=" O PHE J 387 " (cutoff:3.500A) removed outlier: 3.993A 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: 3.777A pdb=" N ILE K 164 " --> pdb=" O THR K 160 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN K 166 " --> pdb=" O GLN K 162 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS K 167 " --> pdb=" O ILE K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 177 removed outlier: 4.404A pdb=" N GLU K 176 " --> pdb=" O ASP K 172 " (cutoff:3.500A) removed outlier: 4.050A 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 193 removed outlier: 3.610A pdb=" N ASN K 193 " --> pdb=" O ASP K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 207 removed outlier: 3.660A 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 232 Processing helix chain 'K' and resid 232 through 237 removed outlier: 4.013A pdb=" N PHE K 236 " --> pdb=" O LEU K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 275 removed outlier: 3.515A pdb=" N VAL K 263 " --> pdb=" O ASP K 259 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP K 265 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N CYS K 266 " --> pdb=" O THR K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 309 removed outlier: 3.618A pdb=" N GLU K 309 " --> pdb=" O GLN K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 334 removed outlier: 3.937A pdb=" N LEU K 329 " --> pdb=" O THR K 325 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER K 334 " --> pdb=" O ILE K 330 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 355 removed outlier: 3.683A pdb=" N GLU K 351 " --> pdb=" O ASP K 347 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER K 355 " --> pdb=" O GLU K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 394 removed outlier: 4.126A pdb=" N LYS K 391 " --> pdb=" O PHE K 387 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU K 392 " --> pdb=" O ALA K 388 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE K 393 " --> pdb=" O ASP K 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 169 removed outlier: 4.000A pdb=" N ILE L 163 " --> pdb=" O GLU L 159 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 177 removed outlier: 3.580A pdb=" N HIS L 177 " --> pdb=" O TYR L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 192 removed outlier: 3.530A pdb=" N ASP L 189 " --> pdb=" O ARG L 185 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE L 190 " --> pdb=" O LYS L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 209 removed outlier: 3.559A pdb=" N ILE L 208 " --> pdb=" O PHE L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 217 through 222 removed outlier: 4.033A pdb=" N GLN L 221 " --> pdb=" O ILE L 217 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR L 222 " --> pdb=" O TRP L 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 217 through 222' Processing helix chain 'L' and resid 224 through 237 removed outlier: 3.642A pdb=" N SER L 235 " --> pdb=" O LYS L 231 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE L 236 " --> pdb=" O LEU L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 274 removed outlier: 3.624A pdb=" N CYS L 266 " --> pdb=" O THR L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 309 removed outlier: 3.728A pdb=" N GLU L 309 " --> pdb=" O GLN L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 335 removed outlier: 3.725A pdb=" N SER L 334 " --> pdb=" O ILE L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 345 through 355 removed outlier: 3.711A pdb=" N GLU L 351 " --> pdb=" O ASP L 347 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN L 354 " --> pdb=" O ASN L 350 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER L 355 " --> pdb=" O GLU L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 386 through 393 removed outlier: 3.656A pdb=" N LYS L 391 " --> pdb=" O ALA L 388 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE L 393 " --> pdb=" O ILE L 390 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 236 removed outlier: 4.248A pdb=" N PHE M 236 " --> pdb=" O LEU M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 244 Processing helix chain 'M' and resid 259 through 274 removed outlier: 3.725A pdb=" N VAL M 263 " --> pdb=" O ASP M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 309 Processing helix chain 'M' and resid 325 through 335 removed outlier: 4.029A pdb=" N LEU M 329 " --> pdb=" O THR M 325 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER M 334 " --> pdb=" O ILE M 330 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 354 removed outlier: 3.553A pdb=" N ASN M 354 " --> pdb=" O ASN M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 389 through 394 removed outlier: 3.697A pdb=" N ILE M 393 " --> pdb=" O ASP M 389 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 233 removed outlier: 3.695A pdb=" N LEU N 229 " --> pdb=" O ARG N 225 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU N 232 " --> pdb=" O TYR N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 274 removed outlier: 3.932A 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: 4.102A pdb=" N LEU N 329 " --> pdb=" O THR N 325 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER N 334 " --> pdb=" O ILE N 330 " (cutoff:3.500A) Processing helix chain 'N' and resid 345 through 356 removed outlier: 3.519A pdb=" N GLU N 351 " --> pdb=" O ASP N 347 " (cutoff:3.500A) 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 236 removed outlier: 3.863A pdb=" N PHE O 236 " --> pdb=" O LEU O 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 259 through 274 removed outlier: 3.739A 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 334 removed outlier: 4.149A pdb=" N LEU O 329 " --> pdb=" O THR O 325 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER O 334 " --> pdb=" O ILE O 330 " (cutoff:3.500A) Processing helix chain 'O' and resid 345 through 354 removed outlier: 3.694A pdb=" N ASN O 354 " --> pdb=" O ASN O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 388 through 394 removed outlier: 4.427A pdb=" N GLU O 392 " --> pdb=" O ALA O 388 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 237 removed outlier: 3.713A pdb=" N LEU P 229 " --> pdb=" O ARG P 225 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE P 236 " --> pdb=" O LEU P 232 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 243 removed outlier: 3.958A pdb=" N ASN P 242 " --> pdb=" O ARG P 238 " (cutoff:3.500A) removed outlier: 4.157A 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: 4.093A pdb=" N VAL P 263 " --> pdb=" O ASP P 259 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS P 264 " --> pdb=" O ILE P 260 " (cutoff:3.500A) removed outlier: 3.621A 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 325 through 332 removed outlier: 4.108A pdb=" N LEU P 329 " --> pdb=" O THR P 325 " (cutoff:3.500A) Processing helix chain 'P' and resid 345 through 354 removed outlier: 3.708A 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 237 removed outlier: 3.616A pdb=" N LYS Q 231 " --> pdb=" O GLU Q 227 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU Q 232 " --> pdb=" O TYR Q 228 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS Q 233 " --> pdb=" O LEU Q 229 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE Q 236 " --> pdb=" O LEU Q 232 " (cutoff:3.500A) Processing helix chain 'Q' and resid 259 through 274 Processing helix chain 'Q' and resid 295 through 309 Processing helix chain 'Q' and resid 325 through 335 removed outlier: 3.922A pdb=" N LEU Q 329 " --> pdb=" O THR Q 325 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER Q 334 " --> pdb=" O ILE Q 330 " (cutoff:3.500A) Processing helix chain 'Q' and resid 345 through 354 removed outlier: 3.587A 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: 3.665A pdb=" N ARG R 230 " --> pdb=" O LYS R 226 " (cutoff:3.500A) removed outlier: 3.745A 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 334 removed outlier: 3.882A pdb=" N LEU R 329 " --> pdb=" O THR R 325 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER R 334 " --> pdb=" O ILE R 330 " (cutoff:3.500A) Processing helix chain 'R' and resid 345 through 354 removed outlier: 3.827A 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 7 through 14 removed outlier: 6.533A pdb=" N ASN A 8 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 6.638A 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 26 current: chain 'A' and resid 50 through 62 removed outlier: 7.152A pdb=" N VAL A 50 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS A 82 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 52 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A 80 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA A 54 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE A 78 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE A 56 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER A 76 " --> pdb=" O ILE A 56 " (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: 6.934A pdb=" N VAL B 50 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS B 82 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU B 52 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 80 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ALA B 54 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE B 78 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE B 56 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 6.398A 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 18 through 26 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 26 current: chain 'C' and resid 50 through 62 removed outlier: 6.926A pdb=" N VAL C 50 " --> pdb=" O LYS C 82 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS C 82 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU C 52 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU C 80 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ALA C 54 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE C 78 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE C 56 " --> pdb=" O SER C 76 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N SER C 76 " --> pdb=" O ILE C 56 " (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 26 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 19 through 26 current: chain 'D' and resid 50 through 62 removed outlier: 7.005A pdb=" N VAL D 50 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS D 82 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU D 52 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU D 80 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA D 54 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE D 78 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE D 56 " --> pdb=" O SER D 76 " (cutoff:3.500A) removed outlier: 6.544A 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 18 through 23 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 23 current: chain 'E' and resid 50 through 62 removed outlier: 6.894A pdb=" N VAL E 50 " --> pdb=" O LYS E 82 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS E 82 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU E 52 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU E 80 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ALA E 54 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE E 78 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE E 56 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 6.596A 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: 6.805A pdb=" N ALA F 51 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU F 80 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU F 53 " --> pdb=" O ILE F 78 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU F 74 " --> pdb=" O ASP F 57 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE F 59 " --> pdb=" O MET F 72 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET F 72 " --> pdb=" O PHE F 59 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE F 61 " --> pdb=" O LYS F 70 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS F 70 " --> pdb=" O ILE F 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 138 removed outlier: 7.756A pdb=" N VAL A 135 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE A 124 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N HIS A 146 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ILE A 483 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA A 148 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A 147 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N SER A 465 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 149 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N HIS A 183 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL A 424 " --> pdb=" O HIS A 183 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 185 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLU A 426 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE A 187 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN A 201 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ASP A 379 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 203 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 301 removed outlier: 3.836A pdb=" N ILE A 292 " --> pdb=" O ASP A 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 134 through 138 removed outlier: 7.615A pdb=" N VAL B 135 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE B 124 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 530 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA B 148 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE B 147 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N SER B 465 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 149 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 185 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN B 201 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASP B 379 " --> pdb=" O ASN B 201 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU B 203 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 298 through 301 removed outlier: 3.751A pdb=" N GLU B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 292 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG B 284 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 321 " --> pdb=" O LYS B 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 134 through 138 removed outlier: 7.705A pdb=" N VAL C 135 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE C 124 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 530 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA C 148 " --> pdb=" O ILE C 483 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE C 185 " --> pdb=" O VAL C 424 " (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 Processing sheet with id=AB1, first strand: chain 'D' and resid 134 through 138 removed outlier: 7.754A pdb=" N VAL D 135 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE D 124 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N HIS D 146 " --> pdb=" O CYS D 479 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE D 421 " --> pdb=" O THR D 460 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU D 462 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE D 423 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA D 464 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR D 425 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE D 185 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLU D 426 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE D 187 " --> pdb=" O GLU D 426 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE D 184 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU D 378 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE D 186 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN D 201 " --> pdb=" O ILE D 377 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASP D 379 " --> pdb=" O ASN D 201 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU D 203 " --> pdb=" O ASP D 379 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 284 through 285 Processing sheet with id=AB3, first strand: chain 'D' and resid 299 through 301 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 138 removed outlier: 4.538A pdb=" N SER E 125 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL E 137 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N THR E 123 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE E 147 " --> pdb=" O LEU E 463 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N SER E 465 " --> pdb=" O ILE E 147 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE E 149 " --> pdb=" O SER E 465 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE E 185 " --> pdb=" O VAL E 424 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLU E 426 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE E 187 " --> pdb=" O GLU E 426 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE E 184 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU E 378 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE E 186 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN E 201 " --> pdb=" O ILE E 375 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 284 through 285 Processing sheet with id=AB6, first strand: chain 'E' and resid 299 through 301 Processing sheet with id=AB7, first strand: chain 'F' and resid 134 through 138 removed outlier: 7.694A pdb=" N VAL F 135 " --> pdb=" O PHE F 124 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE F 124 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER F 530 " --> pdb=" O ILE F 521 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F 521 " --> pdb=" O SER F 530 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA F 148 " --> pdb=" O ILE F 483 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE F 421 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU F 462 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE F 423 " --> pdb=" O LEU F 462 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ALA F 464 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR F 425 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE F 185 " --> pdb=" O VAL F 424 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLU F 426 " --> pdb=" O ILE F 185 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE F 187 " --> pdb=" O GLU F 426 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE F 184 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU F 378 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE F 186 " --> pdb=" O LEU F 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 284 through 285 Processing sheet with id=AB9, first strand: chain 'F' and resid 299 through 301 removed outlier: 3.727A pdb=" N ILE F 292 " --> pdb=" O ASP F 318 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 313 through 314 removed outlier: 6.151A pdb=" N THR G 314 " --> pdb=" O PHE G 342 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE G 291 " --> pdb=" O ILE G 343 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA G 247 " --> pdb=" O GLU G 361 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N TYR G 363 " --> pdb=" O ALA G 247 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE G 249 " --> pdb=" O TYR G 363 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE G 365 " --> pdb=" O PHE G 249 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE G 251 " --> pdb=" O PHE G 365 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 212 through 213 removed outlier: 6.220A pdb=" N ALA H 247 " --> pdb=" O GLU H 361 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N TYR H 363 " --> pdb=" O ALA H 247 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE H 249 " --> pdb=" O TYR H 363 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE H 365 " --> pdb=" O PHE H 249 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE H 251 " --> pdb=" O PHE H 365 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG H 248 " --> pdb=" O PHE H 288 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU H 290 " --> pdb=" O ARG H 248 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE H 250 " --> pdb=" O LEU H 290 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N HIS H 292 " --> pdb=" O PHE H 250 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU H 252 " --> pdb=" O HIS H 292 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE H 291 " --> pdb=" O ILE H 343 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR H 314 " --> pdb=" O PHE H 342 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 313 through 314 removed outlier: 6.261A pdb=" N THR I 314 " --> pdb=" O PHE I 342 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU I 289 " --> pdb=" O ILE I 343 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS I 292 " --> pdb=" O LEU I 252 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA I 247 " --> pdb=" O GLU I 361 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N TYR I 363 " --> pdb=" O ALA I 247 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE I 249 " --> pdb=" O TYR I 363 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N PHE I 365 " --> pdb=" O PHE I 249 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE I 251 " --> pdb=" O PHE I 365 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 313 through 314 removed outlier: 6.372A pdb=" N THR J 314 " --> pdb=" O PHE J 342 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU J 289 " --> pdb=" O ILE J 343 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA J 247 " --> pdb=" O GLU J 361 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N TYR J 363 " --> pdb=" O ALA J 247 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE J 249 " --> pdb=" O TYR J 363 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE J 365 " --> pdb=" O PHE J 249 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE J 251 " --> pdb=" O PHE J 365 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 313 through 314 removed outlier: 6.261A pdb=" N THR K 314 " --> pdb=" O PHE K 342 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE K 291 " --> pdb=" O ILE K 343 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA K 247 " --> pdb=" O GLU K 361 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N TYR K 363 " --> pdb=" O ALA K 247 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE K 249 " --> pdb=" O TYR K 363 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE K 365 " --> pdb=" O PHE K 249 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE K 251 " --> pdb=" O PHE K 365 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 313 through 314 removed outlier: 6.509A pdb=" N THR L 314 " --> pdb=" O PHE L 342 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE L 291 " --> pdb=" O ILE L 343 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG L 248 " --> pdb=" O PHE L 288 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU L 290 " --> pdb=" O ARG L 248 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE L 250 " --> pdb=" O LEU L 290 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N HIS L 292 " --> pdb=" O PHE L 250 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU L 252 " --> pdb=" O HIS L 292 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 313 through 314 removed outlier: 5.860A pdb=" N THR M 314 " --> pdb=" O PHE M 342 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE M 291 " --> pdb=" O ILE M 343 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS M 292 " --> pdb=" O LEU M 252 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA M 247 " --> pdb=" O GLU M 361 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TYR M 363 " --> pdb=" O ALA M 247 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE M 249 " --> pdb=" O TYR M 363 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N PHE M 365 " --> pdb=" O PHE M 249 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE M 251 " --> pdb=" O PHE M 365 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N VAL M 380 " --> pdb=" O LYS M 360 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL M 362 " --> pdb=" O VAL M 380 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE M 382 " --> pdb=" O VAL M 362 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN M 364 " --> pdb=" O ILE M 382 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 313 through 314 removed outlier: 6.032A pdb=" N THR N 314 " --> pdb=" O PHE N 342 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE N 291 " --> pdb=" O ILE N 343 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA N 247 " --> pdb=" O GLU N 361 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N TYR N 363 " --> pdb=" O ALA N 247 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE N 249 " --> pdb=" O TYR N 363 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N PHE N 365 " --> pdb=" O PHE N 249 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE N 251 " --> pdb=" O PHE N 365 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N VAL N 380 " --> pdb=" O LYS N 360 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL N 362 " --> pdb=" O VAL N 380 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE N 382 " --> pdb=" O VAL N 362 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN N 364 " --> pdb=" O ILE N 382 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 313 through 314 removed outlier: 6.054A pdb=" N THR O 314 " --> pdb=" O PHE O 342 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE O 291 " --> pdb=" O ILE O 343 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA O 247 " --> pdb=" O GLU O 361 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N TYR O 363 " --> pdb=" O ALA O 247 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE O 249 " --> pdb=" O TYR O 363 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE O 365 " --> pdb=" O PHE O 249 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE O 251 " --> pdb=" O PHE O 365 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N VAL O 380 " --> pdb=" O LYS O 360 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL O 362 " --> pdb=" O VAL O 380 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE O 382 " --> pdb=" O VAL O 362 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN O 364 " --> pdb=" O ILE O 382 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 313 through 314 removed outlier: 6.199A pdb=" N THR P 314 " --> pdb=" O PHE P 342 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE P 291 " --> pdb=" O ILE P 343 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA P 247 " --> pdb=" O GLU P 361 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N TYR P 363 " --> pdb=" O ALA P 247 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE P 249 " --> pdb=" O TYR P 363 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE P 365 " --> pdb=" O PHE P 249 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE P 251 " --> pdb=" O PHE P 365 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N VAL P 380 " --> pdb=" O LYS P 360 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL P 362 " --> pdb=" O VAL P 380 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE P 382 " --> pdb=" O VAL P 362 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN P 364 " --> pdb=" O ILE P 382 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 313 through 314 removed outlier: 5.889A pdb=" N THR Q 314 " --> pdb=" O PHE Q 342 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE Q 291 " --> pdb=" O ILE Q 343 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA Q 247 " --> pdb=" O GLU Q 361 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N TYR Q 363 " --> pdb=" O ALA Q 247 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE Q 249 " --> pdb=" O TYR Q 363 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N PHE Q 365 " --> pdb=" O PHE Q 249 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE Q 251 " --> pdb=" O PHE Q 365 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N VAL Q 380 " --> pdb=" O LYS Q 360 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL Q 362 " --> pdb=" O VAL Q 380 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE Q 382 " --> pdb=" O VAL Q 362 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN Q 364 " --> pdb=" O ILE Q 382 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 313 through 314 removed outlier: 6.036A pdb=" N THR R 314 " --> pdb=" O PHE R 342 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE R 291 " --> pdb=" O ILE R 343 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA R 247 " --> pdb=" O GLU R 361 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR R 363 " --> pdb=" O ALA R 247 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE R 249 " --> pdb=" O TYR R 363 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE R 365 " --> pdb=" O PHE R 249 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE R 251 " --> pdb=" O PHE R 365 " (cutoff:3.500A) 1698 hydrogen bonds defined for protein. 4812 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: 17.54 Time building geometry restraints manager: 10.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 15706 1.34 - 1.49: 13269 1.49 - 1.64: 20982 1.64 - 1.80: 43 1.80 - 1.95: 75 Bond restraints: 50075 Sorted by residual: bond pdb=" CG PRO C 490 " pdb=" CD PRO C 490 " ideal model delta sigma weight residual 1.503 1.187 0.316 3.40e-02 8.65e+02 8.66e+01 bond pdb=" O3' DT S 3 " pdb=" P DT S 4 " ideal model delta sigma weight residual 1.607 1.548 0.059 1.50e-02 4.44e+03 1.54e+01 bond pdb=" O3' DT S 4 " pdb=" P DT S 5 " ideal model delta sigma weight residual 1.607 1.551 0.056 1.50e-02 4.44e+03 1.38e+01 bond pdb=" P DT S 4 " pdb=" OP1 DT S 4 " ideal model delta sigma weight residual 1.480 1.416 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" N GLU B 290 " pdb=" CA GLU B 290 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.23e-02 6.61e+03 6.86e+00 ... (remaining 50070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.67: 67414 4.67 - 9.34: 280 9.34 - 14.01: 14 14.01 - 18.68: 4 18.68 - 23.35: 2 Bond angle restraints: 67714 Sorted by residual: angle pdb=" N PRO C 490 " pdb=" CD PRO C 490 " pdb=" CG PRO C 490 " ideal model delta sigma weight residual 103.20 79.85 23.35 1.50e+00 4.44e-01 2.42e+02 angle pdb=" O3' DA T 9 " pdb=" C3' DA T 9 " pdb=" C2' DA T 9 " ideal model delta sigma weight residual 111.50 93.80 17.70 1.50e+00 4.44e-01 1.39e+02 angle pdb=" C4' DA T 10 " pdb=" C3' DA T 10 " pdb=" O3' DA T 10 " ideal model delta sigma weight residual 110.00 92.97 17.03 1.50e+00 4.44e-01 1.29e+02 angle pdb=" C4' DT S 3 " pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " ideal model delta sigma weight residual 110.00 93.73 16.27 1.50e+00 4.44e-01 1.18e+02 angle pdb=" CA PRO C 490 " pdb=" CB PRO C 490 " pdb=" CG PRO C 490 " ideal model delta sigma weight residual 104.50 85.32 19.18 1.90e+00 2.77e-01 1.02e+02 ... (remaining 67709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.60: 28528 30.60 - 61.19: 1708 61.19 - 91.79: 109 91.79 - 122.39: 3 122.39 - 152.99: 1 Dihedral angle restraints: 30349 sinusoidal: 12919 harmonic: 17430 Sorted by residual: dihedral pdb=" C5' ADP F 601 " pdb=" O5' ADP F 601 " pdb=" PA ADP F 601 " pdb=" O2A ADP F 601 " ideal model delta sinusoidal sigma weight residual 300.00 147.02 152.99 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" C5' ADP E 601 " pdb=" O5' ADP E 601 " pdb=" PA ADP E 601 " pdb=" O2A ADP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 -175.69 115.69 1 2.00e+01 2.50e-03 3.44e+01 dihedral pdb=" C ASN B 289 " pdb=" N ASN B 289 " pdb=" CA ASN B 289 " pdb=" CB ASN B 289 " ideal model delta harmonic sigma weight residual -122.60 -135.92 13.32 0 2.50e+00 1.60e-01 2.84e+01 ... (remaining 30346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 6739 0.090 - 0.179: 607 0.179 - 0.269: 23 0.269 - 0.358: 8 0.358 - 0.448: 8 Chirality restraints: 7385 Sorted by residual: chirality pdb=" CA ASN B 289 " pdb=" N ASN B 289 " pdb=" C ASN B 289 " pdb=" CB ASN B 289 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C3' DT S 3 " pdb=" C4' DT S 3 " pdb=" O3' DT S 3 " pdb=" C2' DT S 3 " both_signs ideal model delta sigma weight residual False -2.66 -3.10 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" C4' DA T 9 " pdb=" C5' DA T 9 " pdb=" O4' DA T 9 " pdb=" C3' DA T 9 " both_signs ideal model delta sigma weight residual False -2.53 -2.10 -0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 7382 not shown) Planarity restraints: 8640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 253 " 0.077 5.00e-02 4.00e+02 1.16e-01 2.17e+01 pdb=" N PRO F 254 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO F 254 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO F 254 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR Q 325 " -0.071 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO Q 326 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO Q 326 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO Q 326 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC S 2 " -0.054 2.00e-02 2.50e+03 2.82e-02 1.79e+01 pdb=" N1 DC S 2 " 0.048 2.00e-02 2.50e+03 pdb=" C2 DC S 2 " 0.007 2.00e-02 2.50e+03 pdb=" O2 DC S 2 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DC S 2 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DC S 2 " 0.011 2.00e-02 2.50e+03 pdb=" N4 DC S 2 " -0.040 2.00e-02 2.50e+03 pdb=" C5 DC S 2 " 0.012 2.00e-02 2.50e+03 pdb=" C6 DC S 2 " 0.004 2.00e-02 2.50e+03 ... (remaining 8637 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 531 2.58 - 3.16: 37506 3.16 - 3.74: 78699 3.74 - 4.32: 114811 4.32 - 4.90: 189070 Nonbonded interactions: 420617 Sorted by model distance: nonbonded pdb=" O2G AGS C 601 " pdb="MG MG C 602 " model vdw 1.996 2.170 nonbonded pdb=" OG SER C 158 " pdb="MG MG C 602 " model vdw 2.008 2.170 nonbonded pdb=" OG SER E 158 " pdb="MG MG E 602 " model vdw 2.009 2.170 nonbonded pdb=" O2G AGS A 601 " pdb="MG MG A 602 " model vdw 2.020 2.170 nonbonded pdb=" OG SER B 158 " pdb="MG MG B 602 " model vdw 2.022 2.170 ... (remaining 420612 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: 1.380 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: 0.030 Extract box with map and model: 1.450 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 85.590 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 0.316 50075 Z= 0.316 Angle : 0.827 23.347 67714 Z= 0.447 Chirality : 0.053 0.448 7385 Planarity : 0.006 0.116 8640 Dihedral : 17.836 152.986 19027 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.50 % Favored : 97.49 % Rotamer: Outliers : 0.29 % Allowed : 26.16 % Favored : 73.55 % Cbeta Deviations : 0.02 % 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: -1.94 (0.10), residues: 5849 helix: -2.32 (0.08), residues: 2188 sheet: 0.25 (0.17), residues: 915 loop : -0.76 (0.11), residues: 2746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 556 HIS 0.017 0.002 HIS A 232 PHE 0.027 0.002 PHE D 122 TYR 0.041 0.002 TYR H 366 ARG 0.018 0.001 ARG J 225 *********************** 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 678 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 662 time to evaluate : 4.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.8439 (m-30) cc_final: 0.8196 (m-30) REVERT: B 287 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7527 (mppt) REVERT: C 30 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7943 (mmtm) REVERT: D 13 SER cc_start: 0.9302 (p) cc_final: 0.8958 (m) REVERT: D 473 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7814 (mt-10) REVERT: G 279 LYS cc_start: 0.8434 (pttt) cc_final: 0.8152 (pptt) REVERT: G 346 ILE cc_start: 0.8714 (mp) cc_final: 0.8473 (mp) REVERT: H 255 GLN cc_start: 0.7756 (mt0) cc_final: 0.7467 (mt0) REVERT: I 315 ASP cc_start: 0.8255 (p0) cc_final: 0.7852 (p0) REVERT: N 230 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7546 (ppt90) REVERT: O 280 ARG cc_start: 0.7067 (mtt180) cc_final: 0.6834 (mtt-85) REVERT: O 369 ASN cc_start: 0.7746 (m-40) cc_final: 0.7253 (t0) REVERT: Q 243 THR cc_start: 0.7785 (p) cc_final: 0.7556 (t) REVERT: R 279 LYS cc_start: 0.8149 (ptpt) cc_final: 0.7725 (ptmm) REVERT: R 301 GLU cc_start: 0.8343 (tp30) cc_final: 0.8131 (tp30) outliers start: 16 outliers final: 2 residues processed: 674 average time/residue: 1.3209 time to fit residues: 1111.2138 Evaluate side-chains 572 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 569 time to evaluate : 4.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain Q residue 342 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 493 optimal weight: 0.4980 chunk 442 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 298 optimal weight: 0.0970 chunk 236 optimal weight: 5.9990 chunk 457 optimal weight: 9.9990 chunk 177 optimal weight: 0.7980 chunk 278 optimal weight: 2.9990 chunk 340 optimal weight: 7.9990 chunk 530 optimal weight: 7.9990 overall best weight: 2.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 195 ASN A 232 HIS A 251 GLN A 304 ASN A 308 HIS B 140 ASN B 337 GLN B 405 HIS C 183 HIS C 263 HIS C 278 ASN ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN D 195 ASN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 ASN D 509 ASN E 58 ASN E 144 ASN E 263 HIS ** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN F 374 ASN G 305 GLN G 369 ASN ** G 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 383 GLN J 305 GLN K 255 GLN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 216 ASN L 271 GLN M 271 GLN M 305 GLN M 364 GLN ** N 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 50075 Z= 0.284 Angle : 0.576 11.173 67714 Z= 0.309 Chirality : 0.046 0.188 7385 Planarity : 0.005 0.071 8640 Dihedral : 8.913 134.792 6736 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.32 % Allowed : 24.02 % Favored : 72.65 % 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: -0.73 (0.10), residues: 5849 helix: -0.44 (0.10), residues: 2219 sheet: 0.20 (0.17), residues: 947 loop : -0.64 (0.11), residues: 2683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 218 HIS 0.006 0.001 HIS C 146 PHE 0.020 0.002 PHE L 184 TYR 0.023 0.002 TYR I 366 ARG 0.009 0.001 ARG F 309 *********************** 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 828 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 646 time to evaluate : 4.375 Fit side-chains revert: symmetry clash REVERT: A 170 ASP cc_start: 0.8348 (m-30) cc_final: 0.8146 (m-30) REVERT: A 522 MET cc_start: 0.8970 (ptp) cc_final: 0.8703 (ptp) REVERT: B 5 ASN cc_start: 0.6068 (OUTLIER) cc_final: 0.5598 (t0) REVERT: B 463 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8195 (mp) REVERT: B 548 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.8223 (t80) REVERT: C 74 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7788 (tt0) REVERT: C 106 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7445 (p0) REVERT: C 546 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7186 (pt) REVERT: D 62 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: D 383 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8247 (m) REVERT: D 476 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: D 500 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7218 (tt) REVERT: E 27 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7657 (tp30) REVERT: E 144 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7375 (t0) REVERT: E 222 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: E 412 LYS cc_start: 0.7849 (mtmt) cc_final: 0.7595 (mmpt) REVERT: G 279 LYS cc_start: 0.8566 (pttt) cc_final: 0.8258 (pptt) REVERT: I 315 ASP cc_start: 0.8449 (p0) cc_final: 0.7969 (p0) REVERT: K 220 TYR cc_start: 0.7522 (t80) cc_final: 0.7288 (t80) REVERT: L 283 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7954 (mtp85) REVERT: M 383 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: O 280 ARG cc_start: 0.7103 (mtt180) cc_final: 0.6874 (mtt-85) REVERT: O 369 ASN cc_start: 0.7703 (m-40) cc_final: 0.7091 (t0) REVERT: Q 243 THR cc_start: 0.7732 (p) cc_final: 0.7515 (t) REVERT: Q 298 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7503 (p0) REVERT: Q 361 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8459 (mt-10) REVERT: R 279 LYS cc_start: 0.8223 (ptpt) cc_final: 0.7805 (ptmm) REVERT: R 376 GLN cc_start: 0.8683 (pm20) cc_final: 0.8387 (pm20) outliers start: 182 outliers final: 58 residues processed: 776 average time/residue: 1.2833 time to fit residues: 1250.3105 Evaluate side-chains 637 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 563 time to evaluate : 4.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 476 PHE Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain K residue 347 ASP Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 256 ASP Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 367 THR Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain P residue 375 SER Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 258 THR Chi-restraints excluded: chain Q residue 298 ASN Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 360 LYS Chi-restraints excluded: chain Q residue 361 GLU Chi-restraints excluded: chain R residue 257 LYS Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 375 SER Chi-restraints excluded: chain R residue 380 VAL Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 294 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 441 optimal weight: 3.9990 chunk 361 optimal weight: 20.0000 chunk 146 optimal weight: 0.3980 chunk 531 optimal weight: 8.9990 chunk 573 optimal weight: 5.9990 chunk 473 optimal weight: 0.8980 chunk 526 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 426 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 304 ASN B 278 ASN C 240 GLN C 278 ASN D 195 ASN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 ASN E 181 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS ** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN F 67 GLN ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 305 GLN G 369 ASN I 177 HIS I 255 GLN ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 305 GLN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 308 ASN M 271 GLN ** M 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 305 GLN P 364 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 50075 Z= 0.228 Angle : 0.511 9.557 67714 Z= 0.273 Chirality : 0.044 0.160 7385 Planarity : 0.004 0.060 8640 Dihedral : 8.580 132.372 6730 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.47 % Allowed : 23.93 % Favored : 72.60 % 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: -0.32 (0.11), residues: 5849 helix: 0.26 (0.11), residues: 2257 sheet: 0.02 (0.17), residues: 948 loop : -0.59 (0.11), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 556 HIS 0.005 0.001 HIS K 292 PHE 0.022 0.001 PHE L 184 TYR 0.013 0.001 TYR I 366 ARG 0.008 0.000 ARG J 238 *********************** 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 816 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 626 time to evaluate : 4.606 Fit side-chains revert: symmetry clash REVERT: A 170 ASP cc_start: 0.8349 (m-30) cc_final: 0.8099 (m-30) REVERT: A 343 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7953 (mtmm) REVERT: B 5 ASN cc_start: 0.6233 (OUTLIER) cc_final: 0.5751 (t0) REVERT: B 248 ILE cc_start: 0.8884 (mm) cc_final: 0.8664 (mp) REVERT: B 338 SER cc_start: 0.7601 (t) cc_final: 0.7372 (m) REVERT: B 548 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7938 (t80) REVERT: C 74 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7815 (tt0) REVERT: C 106 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7438 (p0) REVERT: C 129 LEU cc_start: 0.8275 (mt) cc_final: 0.8022 (mt) REVERT: C 466 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: C 546 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7191 (pt) REVERT: D 62 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: D 314 ASN cc_start: 0.7886 (OUTLIER) cc_final: 0.7510 (p0) REVERT: D 463 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8712 (mp) REVERT: D 476 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: D 563 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8207 (tttt) REVERT: E 18 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8257 (tppt) REVERT: E 222 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: E 351 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7721 (mm-30) REVERT: E 412 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7571 (mmpt) REVERT: E 439 LYS cc_start: 0.7999 (ptmt) cc_final: 0.7776 (pttp) REVERT: E 542 SER cc_start: 0.8647 (OUTLIER) cc_final: 0.8439 (m) REVERT: F 328 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8177 (mmtp) REVERT: G 279 LYS cc_start: 0.8535 (pttt) cc_final: 0.8269 (pptt) REVERT: H 255 GLN cc_start: 0.7760 (mt0) cc_final: 0.7388 (mt0) REVERT: H 322 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8291 (p) REVERT: I 214 LEU cc_start: 0.7725 (mm) cc_final: 0.7430 (mp) REVERT: I 315 ASP cc_start: 0.8497 (p0) cc_final: 0.8057 (p0) REVERT: J 331 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6903 (mm-30) REVERT: L 283 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7935 (mtp85) REVERT: M 253 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8541 (tm-30) REVERT: M 383 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: N 371 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8341 (mp) REVERT: N 376 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: O 280 ARG cc_start: 0.7096 (mtt180) cc_final: 0.6868 (mtt-85) REVERT: O 337 GLU cc_start: 0.7731 (mp0) cc_final: 0.7406 (mp0) REVERT: O 369 ASN cc_start: 0.7753 (m-40) cc_final: 0.7178 (t0) REVERT: O 383 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: Q 243 THR cc_start: 0.7687 (p) cc_final: 0.7481 (t) REVERT: Q 361 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8500 (mt-10) REVERT: R 253 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8043 (tm-30) REVERT: R 279 LYS cc_start: 0.8247 (ptpt) cc_final: 0.7857 (ptmm) outliers start: 190 outliers final: 69 residues processed: 760 average time/residue: 1.2353 time to fit residues: 1186.3357 Evaluate side-chains 647 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 556 time to evaluate : 4.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 466 GLN Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 476 PHE Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 569 SER Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 346 ILE 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 344 ASN Chi-restraints excluded: chain K residue 347 ASP Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 256 ASP Chi-restraints excluded: chain L residue 273 ASN Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 376 GLN Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain O residue 383 GLN Chi-restraints excluded: chain P residue 375 SER Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 360 LYS Chi-restraints excluded: chain Q residue 361 GLU Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 524 optimal weight: 1.9990 chunk 399 optimal weight: 6.9990 chunk 275 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 253 optimal weight: 10.0000 chunk 356 optimal weight: 1.9990 chunk 533 optimal weight: 6.9990 chunk 564 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 505 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 304 ASN C 83 ASN C 240 GLN C 278 ASN C 282 ASN D 47 ASN D 67 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 ASN E 181 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN F 195 ASN G 369 ASN H 350 ASN ** I 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 341 GLN ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 GLN J 305 GLN K 216 ASN K 305 GLN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 271 GLN ** M 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 305 GLN P 292 HIS R 242 ASN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 50075 Z= 0.381 Angle : 0.570 8.845 67714 Z= 0.301 Chirality : 0.047 0.189 7385 Planarity : 0.004 0.061 8640 Dihedral : 8.696 139.090 6730 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.06 % Allowed : 23.93 % Favored : 72.01 % 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: -0.37 (0.11), residues: 5849 helix: 0.34 (0.11), residues: 2283 sheet: -0.29 (0.16), residues: 990 loop : -0.64 (0.11), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 213 HIS 0.007 0.001 HIS E 146 PHE 0.023 0.002 PHE L 184 TYR 0.022 0.002 TYR K 220 ARG 0.011 0.001 ARG G 238 *********************** 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 809 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 587 time to evaluate : 4.452 Fit side-chains revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8523 (tptp) REVERT: A 170 ASP cc_start: 0.8423 (m-30) cc_final: 0.8199 (m-30) REVERT: A 343 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7950 (mtmm) REVERT: A 522 MET cc_start: 0.8977 (ptp) cc_final: 0.8617 (ptp) REVERT: A 548 TYR cc_start: 0.9042 (m-80) cc_final: 0.8549 (m-80) REVERT: B 5 ASN cc_start: 0.6406 (OUTLIER) cc_final: 0.5968 (t0) REVERT: B 179 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8626 (pt) REVERT: B 338 SER cc_start: 0.8160 (t) cc_final: 0.7876 (m) REVERT: B 513 SER cc_start: 0.8422 (p) cc_final: 0.8117 (m) REVERT: B 548 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.7687 (t80) REVERT: C 74 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7795 (tt0) REVERT: C 257 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8293 (tttt) REVERT: C 466 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.7946 (mp10) REVERT: C 476 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8293 (m-80) REVERT: D 62 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: D 314 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7569 (p0) REVERT: D 476 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: E 35 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8685 (mmtm) REVERT: E 222 GLU cc_start: 0.7716 (tp30) cc_final: 0.7486 (tt0) REVERT: E 351 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7760 (mm-30) REVERT: E 412 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7587 (mmpt) REVERT: F 27 GLU cc_start: 0.7593 (mp0) cc_final: 0.7385 (mp0) REVERT: F 328 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8277 (mmtp) REVERT: G 279 LYS cc_start: 0.8578 (pttt) cc_final: 0.8353 (pptt) REVERT: H 322 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8368 (p) REVERT: I 153 PHE cc_start: 0.2311 (OUTLIER) cc_final: 0.0895 (m-80) REVERT: I 255 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6820 (mp10) REVERT: I 315 ASP cc_start: 0.8614 (p0) cc_final: 0.8233 (p0) REVERT: J 230 ARG cc_start: 0.7861 (ttp-170) cc_final: 0.7558 (ttp-170) REVERT: J 331 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6999 (mm-30) REVERT: K 385 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7603 (ttpp) REVERT: L 283 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7976 (mtp85) REVERT: M 299 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8903 (tm) REVERT: M 383 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: N 376 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8139 (pm20) REVERT: O 280 ARG cc_start: 0.7148 (mtt180) cc_final: 0.6903 (mtt-85) REVERT: P 376 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7910 (pm20) REVERT: Q 243 THR cc_start: 0.7815 (p) cc_final: 0.7545 (t) REVERT: Q 361 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8590 (mt-10) REVERT: R 253 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8130 (tm-30) REVERT: R 279 LYS cc_start: 0.8307 (ptpt) cc_final: 0.7904 (ptmm) outliers start: 222 outliers final: 112 residues processed: 736 average time/residue: 1.2885 time to fit residues: 1191.9923 Evaluate side-chains 671 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 535 time to evaluate : 4.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 466 GLN Chi-restraints excluded: chain C residue 476 PHE Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 476 PHE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain E residue 524 ASP Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 569 SER Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 286 SER Chi-restraints excluded: chain H residue 322 SER 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 255 GLN Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 346 ILE Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 347 ASP Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain K residue 385 LYS Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 256 ASP Chi-restraints excluded: chain L residue 273 ASN Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 393 ILE Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 376 GLN Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 375 SER Chi-restraints excluded: chain P residue 376 GLN Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain Q residue 258 THR Chi-restraints excluded: chain Q residue 283 ARG Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 361 GLU Chi-restraints excluded: chain Q residue 375 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 257 LYS Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain R residue 375 SER Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 470 optimal weight: 5.9990 chunk 320 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 420 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 481 optimal weight: 20.0000 chunk 390 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 506 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 304 ASN A 306 ASN C 245 ASN C 249 HIS C 278 ASN C 281 ASN C 282 ASN D 240 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 ASN E 195 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN G 369 ASN H 255 GLN ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 HIS K 305 GLN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 271 GLN ** M 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 379 GLN N 354 ASN ** N 381 ASN ** 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 50075 Z= 0.416 Angle : 0.579 9.103 67714 Z= 0.305 Chirality : 0.047 0.191 7385 Planarity : 0.004 0.060 8640 Dihedral : 8.784 141.376 6729 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.53 % Allowed : 24.10 % Favored : 71.37 % 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: -0.40 (0.11), residues: 5849 helix: 0.36 (0.11), residues: 2289 sheet: -0.42 (0.16), residues: 978 loop : -0.65 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 274 HIS 0.007 0.001 HIS K 292 PHE 0.025 0.002 PHE L 184 TYR 0.023 0.002 TYR K 220 ARG 0.011 0.001 ARG G 238 *********************** 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 803 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 555 time to evaluate : 4.478 Fit side-chains revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8554 (tptp) REVERT: A 65 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7514 (tp30) REVERT: A 170 ASP cc_start: 0.8404 (m-30) cc_final: 0.8197 (m-30) REVERT: A 312 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7734 (mttt) REVERT: A 343 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7974 (mtmm) REVERT: A 548 TYR cc_start: 0.9075 (m-80) cc_final: 0.8599 (m-80) REVERT: B 5 ASN cc_start: 0.6394 (OUTLIER) cc_final: 0.6009 (t0) REVERT: B 179 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8647 (pt) REVERT: B 548 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.7760 (t80) REVERT: C 74 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7834 (tt0) REVERT: C 257 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8191 (ttmt) REVERT: D 62 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: D 314 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7585 (p0) REVERT: D 476 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: E 222 GLU cc_start: 0.7774 (tp30) cc_final: 0.7535 (tt0) REVERT: E 412 LYS cc_start: 0.7879 (mtmt) cc_final: 0.7541 (mmpt) REVERT: E 440 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.6792 (m-80) REVERT: F 65 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: F 328 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8255 (mmtp) REVERT: G 198 ARG cc_start: 0.3834 (OUTLIER) cc_final: 0.2494 (tpt170) REVERT: G 279 LYS cc_start: 0.8556 (pttt) cc_final: 0.8325 (pptt) REVERT: I 153 PHE cc_start: 0.2418 (OUTLIER) cc_final: 0.1012 (m-80) REVERT: I 255 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6848 (mp10) REVERT: I 315 ASP cc_start: 0.8573 (p0) cc_final: 0.8294 (p0) REVERT: I 382 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8146 (mp) REVERT: J 331 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7028 (mm-30) REVERT: K 385 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7712 (tttm) REVERT: L 283 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7992 (mtp85) REVERT: L 359 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7047 (ttt180) REVERT: M 383 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: N 279 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7786 (ptpp) REVERT: N 380 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8776 (t) REVERT: O 280 ARG cc_start: 0.7156 (mtt180) cc_final: 0.6904 (mtt-85) REVERT: O 369 ASN cc_start: 0.7893 (m-40) cc_final: 0.7236 (t0) REVERT: Q 243 THR cc_start: 0.7765 (p) cc_final: 0.7512 (t) REVERT: Q 361 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8584 (mt-10) REVERT: R 253 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8138 (tm-30) REVERT: R 279 LYS cc_start: 0.8314 (ptpt) cc_final: 0.7902 (ptmm) outliers start: 248 outliers final: 131 residues processed: 731 average time/residue: 1.2752 time to fit residues: 1175.6791 Evaluate side-chains 678 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 520 time to evaluate : 4.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 548 TYR 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 38 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 476 PHE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 440 TYR Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 524 ASP Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 569 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 530 SER Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain G residue 198 ARG Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 286 SER 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 255 GLN Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 346 ILE Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 347 ASP Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain K residue 385 LYS Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 256 ASP Chi-restraints excluded: chain L residue 273 ASN Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 325 THR Chi-restraints excluded: chain L residue 359 ARG Chi-restraints excluded: chain L residue 393 ILE Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 279 LYS Chi-restraints excluded: chain N residue 379 GLN Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain P residue 237 ILE Chi-restraints excluded: chain P residue 258 THR Chi-restraints excluded: chain P residue 375 SER Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain Q residue 258 THR Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 361 GLU Chi-restraints excluded: chain Q residue 375 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 252 LEU Chi-restraints excluded: chain R residue 253 GLU Chi-restraints excluded: chain R residue 258 THR Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain R residue 375 SER Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 189 optimal weight: 3.9990 chunk 508 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 331 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 565 optimal weight: 8.9990 chunk 469 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 296 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 304 ASN A 306 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN C 417 GLN D 67 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN F 245 ASN G 369 ASN ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 305 GLN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 271 GLN ** M 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 379 GLN ** N 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 305 GLN Q 379 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 50075 Z= 0.195 Angle : 0.494 9.256 67714 Z= 0.263 Chirality : 0.043 0.151 7385 Planarity : 0.004 0.058 8640 Dihedral : 8.547 140.090 6729 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.53 % Allowed : 25.16 % Favored : 71.32 % 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: 0.63 (0.11), residues: 2296 sheet: -0.35 (0.17), residues: 907 loop : -0.55 (0.11), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 274 HIS 0.008 0.001 HIS C 263 PHE 0.021 0.001 PHE L 184 TYR 0.023 0.001 TYR K 220 ARG 0.013 0.000 ARG G 238 *********************** 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 758 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 565 time to evaluate : 4.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7940 (mtmm) REVERT: A 548 TYR cc_start: 0.9018 (m-80) cc_final: 0.8735 (m-80) REVERT: B 5 ASN cc_start: 0.6240 (OUTLIER) cc_final: 0.5861 (t0) REVERT: B 179 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8390 (pt) REVERT: B 222 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: B 411 ARG cc_start: 0.7424 (tpp80) cc_final: 0.7028 (tpp80) REVERT: B 548 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.7795 (t80) REVERT: C 52 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8560 (mp) REVERT: C 546 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7317 (pt) REVERT: D 62 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: D 314 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7576 (p0) REVERT: D 328 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8217 (mttm) REVERT: D 383 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8321 (m) REVERT: D 476 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: E 222 GLU cc_start: 0.7741 (tp30) cc_final: 0.7537 (tt0) REVERT: E 412 LYS cc_start: 0.7870 (mtmt) cc_final: 0.7535 (mmpt) REVERT: E 440 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.6843 (m-80) REVERT: E 542 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8384 (m) REVERT: F 65 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7303 (tp30) REVERT: F 328 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8293 (mmtp) REVERT: G 225 ARG cc_start: 0.7713 (ttp-170) cc_final: 0.7304 (ttp-110) REVERT: G 279 LYS cc_start: 0.8476 (pttt) cc_final: 0.8215 (pptt) REVERT: I 315 ASP cc_start: 0.8479 (p0) cc_final: 0.8140 (p0) REVERT: I 382 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8010 (mp) REVERT: L 283 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7942 (mtp85) REVERT: M 383 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: N 279 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7762 (ptpp) REVERT: O 280 ARG cc_start: 0.7207 (mtt180) cc_final: 0.6957 (mtt-85) REVERT: O 369 ASN cc_start: 0.7830 (m-40) cc_final: 0.7307 (t0) REVERT: P 376 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: Q 243 THR cc_start: 0.7669 (p) cc_final: 0.7405 (t) REVERT: Q 265 ASP cc_start: 0.8550 (m-30) cc_final: 0.8317 (m-30) REVERT: Q 385 LYS cc_start: 0.7553 (mtmt) cc_final: 0.7216 (mttp) REVERT: R 253 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8089 (tm-30) REVERT: R 279 LYS cc_start: 0.8226 (ptpt) cc_final: 0.7829 (ptmm) outliers start: 193 outliers final: 98 residues processed: 699 average time/residue: 1.2852 time to fit residues: 1129.8269 Evaluate side-chains 647 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 528 time to evaluate : 4.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 436 ASP Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 476 PHE Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 440 TYR Chi-restraints excluded: chain E residue 524 ASP Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 569 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 530 SER Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 347 ASP Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 325 THR Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain M residue 392 GLU Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 279 LYS Chi-restraints excluded: chain N residue 330 ILE Chi-restraints excluded: chain N residue 379 GLN Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 375 SER Chi-restraints excluded: chain P residue 376 GLN Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 544 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 321 optimal weight: 7.9990 chunk 412 optimal weight: 0.0870 chunk 319 optimal weight: 1.9990 chunk 475 optimal weight: 4.9990 chunk 315 optimal weight: 2.9990 chunk 562 optimal weight: 9.9990 chunk 352 optimal weight: 3.9990 chunk 343 optimal weight: 9.9990 chunk 259 optimal weight: 4.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 304 ASN A 306 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN C 282 ASN D 67 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN H 305 GLN ** I 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 177 HIS K 305 GLN K 383 GLN M 242 ASN M 271 GLN ** M 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 379 GLN ** N 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 50075 Z= 0.288 Angle : 0.520 8.351 67714 Z= 0.275 Chirality : 0.045 0.185 7385 Planarity : 0.004 0.057 8640 Dihedral : 8.551 141.433 6729 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.65 % Allowed : 25.28 % Favored : 71.06 % 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: 0.63 (0.11), residues: 2291 sheet: -0.43 (0.17), residues: 978 loop : -0.55 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 213 HIS 0.008 0.001 HIS C 263 PHE 0.027 0.001 PHE I 184 TYR 0.028 0.001 TYR G 220 ARG 0.013 0.000 ARG J 238 *********************** 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 746 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 546 time to evaluate : 4.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 312 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7728 (mttt) REVERT: A 343 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7946 (mtmm) REVERT: A 548 TYR cc_start: 0.9042 (m-80) cc_final: 0.8733 (m-80) REVERT: B 5 ASN cc_start: 0.6341 (OUTLIER) cc_final: 0.5970 (t0) REVERT: B 179 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8461 (pt) REVERT: B 411 ARG cc_start: 0.7441 (tpp80) cc_final: 0.7151 (tpp80) REVERT: B 548 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.7745 (t80) REVERT: C 466 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.7837 (mp10) REVERT: D 62 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: D 314 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7624 (p0) REVERT: D 328 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8231 (mttm) REVERT: D 383 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8161 (m) REVERT: D 476 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: E 25 ASP cc_start: 0.7490 (t0) cc_final: 0.7200 (t70) REVERT: E 412 LYS cc_start: 0.7870 (mtmt) cc_final: 0.7536 (mmpt) REVERT: E 440 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: E 542 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8382 (m) REVERT: F 65 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7318 (tp30) REVERT: F 328 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8181 (mmtp) REVERT: F 441 ARG cc_start: 0.7987 (ppt90) cc_final: 0.7738 (ppt90) REVERT: F 510 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8541 (tp) REVERT: G 225 ARG cc_start: 0.7693 (ttp-170) cc_final: 0.7313 (ttp-110) REVERT: G 279 LYS cc_start: 0.8462 (pttt) cc_final: 0.8221 (pptt) REVERT: I 315 ASP cc_start: 0.8533 (p0) cc_final: 0.8205 (p0) REVERT: I 382 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8007 (mp) REVERT: L 283 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7954 (mtp85) REVERT: M 383 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: N 279 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8026 (mtpt) REVERT: O 280 ARG cc_start: 0.7184 (mtt180) cc_final: 0.6929 (mtt-85) REVERT: O 369 ASN cc_start: 0.7865 (m-40) cc_final: 0.7251 (t0) REVERT: Q 243 THR cc_start: 0.7720 (p) cc_final: 0.7467 (t) REVERT: Q 265 ASP cc_start: 0.8541 (m-30) cc_final: 0.8313 (m-30) REVERT: Q 385 LYS cc_start: 0.7582 (mtmt) cc_final: 0.7238 (mttp) REVERT: R 253 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8103 (tm-30) REVERT: R 279 LYS cc_start: 0.8265 (ptpt) cc_final: 0.7866 (ptmm) outliers start: 200 outliers final: 128 residues processed: 688 average time/residue: 1.2825 time to fit residues: 1119.4737 Evaluate side-chains 671 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 522 time to evaluate : 4.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 548 TYR 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 38 VAL Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 466 GLN Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 436 ASP Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 476 PHE Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 440 TYR Chi-restraints excluded: chain E residue 524 ASP Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 530 SER Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 346 ILE Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 347 ASP Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain K residue 385 LYS Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 256 ASP Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 325 THR Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 279 LYS Chi-restraints excluded: chain N residue 379 GLN Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain O residue 383 GLN Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 375 SER Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 252 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 237 ILE Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 253 GLU Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 348 optimal weight: 0.8980 chunk 224 optimal weight: 0.7980 chunk 336 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 357 optimal weight: 2.9990 chunk 383 optimal weight: 0.9980 chunk 278 optimal weight: 0.0770 chunk 52 optimal weight: 0.0970 chunk 442 optimal weight: 1.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 304 ASN A 306 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN C 417 GLN C 480 ASN D 67 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 ASN E 138 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 305 GLN M 271 GLN ** M 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 273 ASN R 242 ASN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 50075 Z= 0.150 Angle : 0.478 8.659 67714 Z= 0.255 Chirality : 0.042 0.177 7385 Planarity : 0.004 0.058 8640 Dihedral : 8.351 138.062 6729 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.61 % Allowed : 26.43 % Favored : 70.95 % 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: 0.04 (0.11), residues: 5849 helix: 0.80 (0.11), residues: 2304 sheet: -0.36 (0.17), residues: 887 loop : -0.42 (0.12), residues: 2658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 274 HIS 0.007 0.001 HIS C 263 PHE 0.029 0.001 PHE I 184 TYR 0.022 0.001 TYR K 220 ARG 0.013 0.000 ARG J 238 *********************** 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 712 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 569 time to evaluate : 4.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.6876 (ttm-80) cc_final: 0.6644 (ttm110) REVERT: A 309 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7817 (ttp-170) REVERT: A 548 TYR cc_start: 0.8984 (m-80) cc_final: 0.8734 (m-80) REVERT: A 553 ARG cc_start: 0.8469 (mtt90) cc_final: 0.8184 (mtm-85) REVERT: B 312 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8260 (mmtt) REVERT: B 411 ARG cc_start: 0.7365 (tpp80) cc_final: 0.7139 (tpp80) REVERT: B 513 SER cc_start: 0.8503 (p) cc_final: 0.8180 (m) REVERT: B 548 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.7677 (t80) REVERT: C 466 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7788 (mp10) REVERT: C 546 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7254 (pt) REVERT: C 566 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7388 (tp30) REVERT: D 314 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7583 (p0) REVERT: D 383 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8300 (m) REVERT: D 473 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7763 (mt-10) REVERT: D 476 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: E 25 ASP cc_start: 0.7313 (t0) cc_final: 0.6973 (t70) REVERT: E 27 GLU cc_start: 0.7746 (tp30) cc_final: 0.7479 (tp30) REVERT: E 412 LYS cc_start: 0.7835 (mtmt) cc_final: 0.7512 (mmpt) REVERT: F 65 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: F 328 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8281 (mmtp) REVERT: F 441 ARG cc_start: 0.7953 (ppt90) cc_final: 0.7670 (ppt90) REVERT: F 510 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8501 (tp) REVERT: G 225 ARG cc_start: 0.7624 (ttp-170) cc_final: 0.7277 (ttp-110) REVERT: G 231 LYS cc_start: 0.7720 (tmtt) cc_final: 0.7260 (mtmt) REVERT: G 279 LYS cc_start: 0.8452 (pttt) cc_final: 0.8186 (pptt) REVERT: I 214 LEU cc_start: 0.7672 (mm) cc_final: 0.7407 (mp) REVERT: I 315 ASP cc_start: 0.8448 (p0) cc_final: 0.8101 (p0) REVERT: I 382 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8009 (mp) REVERT: M 383 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: N 279 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7968 (mtpt) REVERT: O 280 ARG cc_start: 0.7195 (mtt180) cc_final: 0.6931 (mtt-85) REVERT: O 369 ASN cc_start: 0.7786 (m-40) cc_final: 0.7335 (t0) REVERT: Q 243 THR cc_start: 0.7679 (p) cc_final: 0.7437 (t) REVERT: Q 265 ASP cc_start: 0.8541 (m-30) cc_final: 0.8328 (m-30) REVERT: Q 301 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8162 (tm-30) REVERT: Q 379 GLN cc_start: 0.8941 (mt0) cc_final: 0.8723 (mt0) REVERT: Q 385 LYS cc_start: 0.7530 (mtmt) cc_final: 0.7182 (mttp) REVERT: R 253 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: R 279 LYS cc_start: 0.8206 (ptpt) cc_final: 0.7817 (ptmm) outliers start: 143 outliers final: 75 residues processed: 668 average time/residue: 1.2901 time to fit residues: 1083.1701 Evaluate side-chains 618 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 528 time to evaluate : 4.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 466 GLN Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 566 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 476 PHE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 524 ASP Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 325 THR Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain M residue 392 GLU Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 279 LYS Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain O residue 383 GLN Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 258 THR Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 253 GLU Chi-restraints excluded: chain R residue 257 LYS Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 375 SER Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 512 optimal weight: 0.9990 chunk 539 optimal weight: 8.9990 chunk 491 optimal weight: 3.9990 chunk 524 optimal weight: 7.9990 chunk 315 optimal weight: 7.9990 chunk 228 optimal weight: 1.9990 chunk 411 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 473 optimal weight: 0.6980 chunk 496 optimal weight: 5.9990 chunk 522 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 304 ASN A 306 ASN A 308 HIS ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN C 282 ASN D 67 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN G 221 GLN ** I 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 271 GLN ** M 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 379 GLN ** N 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 50075 Z= 0.340 Angle : 0.555 10.919 67714 Z= 0.291 Chirality : 0.046 0.175 7385 Planarity : 0.004 0.063 8640 Dihedral : 8.515 141.454 6729 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.85 % Allowed : 26.54 % Favored : 70.61 % 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: -0.11 (0.11), residues: 5849 helix: 0.70 (0.11), residues: 2292 sheet: -0.45 (0.17), residues: 978 loop : -0.50 (0.12), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 213 HIS 0.007 0.001 HIS N 292 PHE 0.028 0.002 PHE I 184 TYR 0.023 0.002 TYR K 220 ARG 0.014 0.001 ARG J 238 *********************** 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 690 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 534 time to evaluate : 4.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.6944 (ttm-80) cc_final: 0.6742 (ttm110) REVERT: A 312 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7729 (mttt) REVERT: A 548 TYR cc_start: 0.9052 (m-80) cc_final: 0.8723 (m-80) REVERT: B 5 ASN cc_start: 0.6225 (OUTLIER) cc_final: 0.5994 (t0) REVERT: B 289 ASN cc_start: 0.8503 (t0) cc_final: 0.8295 (t0) REVERT: B 411 ARG cc_start: 0.7445 (tpp80) cc_final: 0.7221 (tpp80) REVERT: B 548 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.7763 (t80) REVERT: C 258 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6676 (pm20) REVERT: C 466 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.7838 (mp10) REVERT: C 566 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7425 (tp30) REVERT: D 62 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: D 106 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7546 (m-30) REVERT: D 314 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7635 (p0) REVERT: D 383 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8243 (m) REVERT: D 476 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8415 (m-80) REVERT: D 563 LYS cc_start: 0.8404 (ptmt) cc_final: 0.8170 (pttp) REVERT: E 25 ASP cc_start: 0.7459 (t0) cc_final: 0.7129 (t70) REVERT: E 412 LYS cc_start: 0.7882 (mtmt) cc_final: 0.7511 (mmpt) REVERT: E 440 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.6779 (m-80) REVERT: E 542 SER cc_start: 0.8535 (t) cc_final: 0.8203 (m) REVERT: F 65 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7317 (tp30) REVERT: F 328 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8244 (mmtp) REVERT: F 441 ARG cc_start: 0.7999 (ppt90) cc_final: 0.7746 (ppt90) REVERT: F 510 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8522 (tp) REVERT: G 279 LYS cc_start: 0.8451 (pttt) cc_final: 0.8229 (pptt) REVERT: I 153 PHE cc_start: 0.1958 (OUTLIER) cc_final: 0.0636 (m-80) REVERT: I 315 ASP cc_start: 0.8566 (p0) cc_final: 0.8283 (p0) REVERT: I 382 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8007 (mp) REVERT: L 283 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7971 (mtp85) REVERT: L 385 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7555 (ttmm) REVERT: M 383 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: M 385 LYS cc_start: 0.7781 (mptt) cc_final: 0.6882 (mptp) REVERT: N 279 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8034 (mtpt) REVERT: O 280 ARG cc_start: 0.7226 (mtt180) cc_final: 0.6971 (mtt-85) REVERT: Q 243 THR cc_start: 0.7776 (p) cc_final: 0.7563 (t) REVERT: Q 265 ASP cc_start: 0.8545 (m-30) cc_final: 0.8309 (m-30) REVERT: Q 385 LYS cc_start: 0.7569 (mtmt) cc_final: 0.7215 (mttp) REVERT: R 253 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8132 (tt0) REVERT: R 279 LYS cc_start: 0.8288 (ptpt) cc_final: 0.7880 (ptmm) outliers start: 156 outliers final: 99 residues processed: 650 average time/residue: 1.2795 time to fit residues: 1043.8483 Evaluate side-chains 634 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 513 time to evaluate : 4.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 5 ASN 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 205 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 466 GLN Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 566 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 476 PHE Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 440 TYR Chi-restraints excluded: chain E residue 524 ASP Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 530 SER Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain I residue 153 PHE Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain K residue 385 LYS Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 256 ASP Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 325 THR Chi-restraints excluded: chain L residue 385 LYS Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 279 LYS Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain O residue 383 GLN Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 258 THR Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 253 GLU Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain R residue 375 SER Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 344 optimal weight: 5.9990 chunk 554 optimal weight: 1.9990 chunk 338 optimal weight: 0.0570 chunk 263 optimal weight: 3.9990 chunk 385 optimal weight: 4.9990 chunk 581 optimal weight: 1.9990 chunk 535 optimal weight: 4.9990 chunk 463 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 357 optimal weight: 1.9990 chunk 284 optimal weight: 4.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 304 ASN A 306 ASN C 245 ASN C 278 ASN D 67 GLN D 195 ASN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN G 305 GLN I 273 ASN ** I 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 305 GLN L 379 GLN M 271 GLN ** M 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 305 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 50075 Z= 0.217 Angle : 0.510 10.469 67714 Z= 0.270 Chirality : 0.043 0.157 7385 Planarity : 0.004 0.059 8640 Dihedral : 8.420 139.015 6729 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.43 % Allowed : 27.02 % Favored : 70.55 % 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: -0.00 (0.11), residues: 5849 helix: 0.76 (0.11), residues: 2309 sheet: -0.40 (0.17), residues: 895 loop : -0.43 (0.12), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 213 HIS 0.006 0.001 HIS C 263 PHE 0.029 0.001 PHE I 184 TYR 0.022 0.001 TYR K 220 ARG 0.016 0.000 ARG H 238 ********************** 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 668 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 535 time to evaluate : 4.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7942 (mtmm) REVERT: A 548 TYR cc_start: 0.9021 (m-80) cc_final: 0.8737 (m-80) REVERT: A 553 ARG cc_start: 0.8488 (mtt90) cc_final: 0.8196 (mtm-85) REVERT: B 5 ASN cc_start: 0.6198 (OUTLIER) cc_final: 0.5987 (t0) REVERT: B 289 ASN cc_start: 0.8473 (t0) cc_final: 0.8233 (t0) REVERT: B 303 ASP cc_start: 0.7171 (p0) cc_final: 0.6803 (p0) REVERT: B 312 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8281 (mmtt) REVERT: B 411 ARG cc_start: 0.7420 (tpp80) cc_final: 0.7131 (tpp80) REVERT: B 548 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.7711 (t80) REVERT: C 258 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6821 (pm20) REVERT: C 466 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7794 (mp10) REVERT: C 546 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7399 (pt) REVERT: C 566 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: D 62 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: D 106 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: D 314 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7582 (p0) REVERT: D 383 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8280 (m) REVERT: D 476 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8340 (m-80) REVERT: D 563 LYS cc_start: 0.8407 (ptmt) cc_final: 0.8164 (pttp) REVERT: E 25 ASP cc_start: 0.7389 (t0) cc_final: 0.7062 (t70) REVERT: E 312 LYS cc_start: 0.7776 (mppt) cc_final: 0.7487 (mmtm) REVERT: E 412 LYS cc_start: 0.7857 (mtmt) cc_final: 0.7344 (mmmt) REVERT: E 440 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.6801 (m-80) REVERT: F 65 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7307 (tp30) REVERT: F 222 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8172 (mt-10) REVERT: F 328 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8245 (mmtp) REVERT: F 441 ARG cc_start: 0.8003 (ppt90) cc_final: 0.7576 (ppt90) REVERT: F 510 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8517 (tp) REVERT: G 225 ARG cc_start: 0.7635 (ttp-170) cc_final: 0.7195 (ttp-110) REVERT: G 231 LYS cc_start: 0.7729 (tmtt) cc_final: 0.7279 (mtmt) REVERT: G 279 LYS cc_start: 0.8488 (pttt) cc_final: 0.8239 (pptt) REVERT: I 153 PHE cc_start: 0.2018 (OUTLIER) cc_final: 0.0731 (m-80) REVERT: I 315 ASP cc_start: 0.8524 (p0) cc_final: 0.8207 (p0) REVERT: I 382 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8035 (mp) REVERT: L 283 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7912 (mtp85) REVERT: M 383 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: N 279 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8028 (mtpt) REVERT: O 280 ARG cc_start: 0.7210 (mtt180) cc_final: 0.6944 (mtt-85) REVERT: O 369 ASN cc_start: 0.7817 (m-40) cc_final: 0.7297 (t0) REVERT: Q 243 THR cc_start: 0.7763 (p) cc_final: 0.7542 (t) REVERT: Q 265 ASP cc_start: 0.8542 (m-30) cc_final: 0.8300 (m-30) REVERT: Q 385 LYS cc_start: 0.7573 (mtmt) cc_final: 0.7210 (mttp) REVERT: R 253 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: R 279 LYS cc_start: 0.8242 (ptpt) cc_final: 0.7839 (ptmm) outliers start: 133 outliers final: 91 residues processed: 628 average time/residue: 1.2917 time to fit residues: 1018.8357 Evaluate side-chains 634 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 520 time to evaluate : 4.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 5 ASN 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 205 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 466 GLN Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 566 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 476 PHE Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 440 TYR Chi-restraints excluded: chain E residue 524 ASP Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 379 GLN Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain I residue 153 PHE Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain K residue 385 LYS Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 325 THR Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 279 LYS Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain O residue 383 GLN Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 258 THR Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 252 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 253 GLU Chi-restraints excluded: chain R residue 334 SER Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain R residue 375 SER Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 368 optimal weight: 9.9990 chunk 493 optimal weight: 4.9990 chunk 141 optimal weight: 0.0770 chunk 427 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 464 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 476 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 304 ASN A 306 ASN B 405 HIS C 234 GLN C 245 ASN C 278 ASN C 417 GLN D 67 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN G 305 GLN I 364 GLN K 166 ASN L 379 GLN M 271 GLN ** M 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 379 GLN N 381 ASN ** 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 = 0.3685 r_free = 0.3685 target = 0.145062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105452 restraints weight = 61276.680| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.01 r_work: 0.3058 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 50075 Z= 0.147 Angle : 0.478 9.783 67714 Z= 0.253 Chirality : 0.042 0.182 7385 Planarity : 0.004 0.059 8640 Dihedral : 8.177 135.635 6729 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.01 % Allowed : 27.49 % Favored : 70.50 % 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: 0.94 (0.11), residues: 2294 sheet: -0.36 (0.18), residues: 896 loop : -0.34 (0.12), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 218 HIS 0.005 0.001 HIS C 263 PHE 0.027 0.001 PHE I 184 TYR 0.021 0.001 TYR K 220 ARG 0.015 0.000 ARG H 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17489.65 seconds wall clock time: 301 minutes 12.44 seconds (18072.44 seconds total)