Starting phenix.real_space_refine on Fri Sep 27 05:07:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuw_37862/09_2024/8wuw_37862.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuw_37862/09_2024/8wuw_37862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuw_37862/09_2024/8wuw_37862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuw_37862/09_2024/8wuw_37862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuw_37862/09_2024/8wuw_37862.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuw_37862/09_2024/8wuw_37862.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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: 7 Type Number sf(0) Gaussians K 7 8.98 5 P 42 5.49 5 Mg 14 5.21 5 S 168 5.16 5 C 40705 2.51 5 N 11172 2.21 5 O 12733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 64841 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "H" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "a" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "h" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 545 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "B" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "I" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "b" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "i" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 545 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "C" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "J" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "c" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "j" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 545 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "D" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "K" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "d" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "k" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 545 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "E" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "L" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "e" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "l" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 545 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "F" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "M" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "f" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "m" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 545 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "G" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "N" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "g" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "n" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 545 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 30.21, per 1000 atoms: 0.47 Number of scatterers: 64841 At special positions: 0 Unit cell: (159.424, 160.176, 259.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 7 19.00 S 168 16.00 P 42 15.00 Mg 14 11.99 O 12733 8.00 N 11172 7.00 C 40705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.83 Conformation dependent library (CDL) restraints added in 6.6 seconds 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15582 Finding SS restraints... Secondary structure from input PDB file: 296 helices and 118 sheets defined 51.1% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.93 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.787A pdb=" N VAL A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.840A pdb=" N GLU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 85 removed outlier: 3.517A pdb=" N GLU A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 109 Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 229 through 244 Proline residue: A 235 - end of helix removed outlier: 3.653A pdb=" N ARG A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 283 through 295 removed outlier: 3.527A pdb=" N ASP A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 357 removed outlier: 3.801A pdb=" N ILE A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 removed outlier: 3.721A pdb=" N LEU A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 410 removed outlier: 3.646A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 removed outlier: 3.945A pdb=" N ALA A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 429 Processing helix chain 'A' and resid 433 through 448 removed outlier: 3.612A pdb=" N ARG A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.724A pdb=" N ARG A 452 " --> pdb=" O ARG A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 476 removed outlier: 4.193A pdb=" N LYS A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 501 through 520 removed outlier: 3.767A pdb=" N THR A 520 " --> pdb=" O GLY A 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 29 removed outlier: 3.652A pdb=" N ALA H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL H 29 " --> pdb=" O ASN H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 59 removed outlier: 3.530A pdb=" N GLU H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 86 removed outlier: 3.697A pdb=" N GLY H 70 " --> pdb=" O TYR H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 109 Processing helix chain 'H' and resid 112 through 135 Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 155 through 170 Processing helix chain 'H' and resid 201 through 205 removed outlier: 3.727A pdb=" N PHE H 204 " --> pdb=" O SER H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 244 Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 255 through 269 Processing helix chain 'H' and resid 283 through 296 removed outlier: 4.013A pdb=" N ASP H 287 " --> pdb=" O GLN H 283 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU H 295 " --> pdb=" O ASP H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 352 Processing helix chain 'H' and resid 356 through 360 removed outlier: 3.610A pdb=" N ASP H 359 " --> pdb=" O THR H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 361 through 373 removed outlier: 4.351A pdb=" N LYS H 371 " --> pdb=" O GLU H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 410 removed outlier: 3.584A pdb=" N GLU H 391 " --> pdb=" O ALA H 387 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS H 392 " --> pdb=" O GLU H 388 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 424 Processing helix chain 'H' and resid 425 through 427 No H-bonds generated for 'chain 'H' and resid 425 through 427' Processing helix chain 'H' and resid 433 through 448 Processing helix chain 'H' and resid 448 through 459 removed outlier: 3.879A pdb=" N ARG H 452 " --> pdb=" O ARG H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 476 removed outlier: 4.022A pdb=" N LYS H 474 " --> pdb=" O LEU H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 492 through 496 Processing helix chain 'H' and resid 501 through 520 Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.796A pdb=" N VAL B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 59 removed outlier: 3.870A pdb=" N GLU B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 85 removed outlier: 3.540A pdb=" N GLU B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 109 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 229 through 244 Proline residue: B 235 - end of helix removed outlier: 4.190A pdb=" N ARG B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 283 through 295 removed outlier: 3.561A pdb=" N ASP B 287 " --> pdb=" O GLN B 283 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 290 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP B 291 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 357 removed outlier: 3.617A pdb=" N ILE B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU B 354 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 374 removed outlier: 3.529A pdb=" N LEU B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 410 removed outlier: 3.665A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 425 removed outlier: 3.948A pdb=" N ALA B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 429 Processing helix chain 'B' and resid 433 through 448 removed outlier: 3.591A pdb=" N ARG B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.728A pdb=" N ARG B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 476 removed outlier: 4.194A pdb=" N LYS B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 501 through 520 removed outlier: 3.757A pdb=" N THR B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 29 removed outlier: 3.653A pdb=" N ALA I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL I 29 " --> pdb=" O ASN I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 59 removed outlier: 3.535A pdb=" N GLU I 59 " --> pdb=" O THR I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 86 removed outlier: 3.607A pdb=" N GLY I 70 " --> pdb=" O TYR I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 109 Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 Processing helix chain 'I' and resid 201 through 205 removed outlier: 3.523A pdb=" N PHE I 204 " --> pdb=" O SER I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 242 Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 255 through 269 Processing helix chain 'I' and resid 283 through 296 removed outlier: 4.322A pdb=" N ASP I 287 " --> pdb=" O GLN I 283 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU I 295 " --> pdb=" O ASP I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 352 Processing helix chain 'I' and resid 356 through 360 Processing helix chain 'I' and resid 361 through 373 removed outlier: 4.052A pdb=" N LYS I 371 " --> pdb=" O GLU I 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 410 Processing helix chain 'I' and resid 416 through 425 removed outlier: 4.130A pdb=" N ALA I 425 " --> pdb=" O ARG I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 448 Processing helix chain 'I' and resid 448 through 459 removed outlier: 3.874A pdb=" N ARG I 452 " --> pdb=" O ARG I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 476 removed outlier: 4.009A pdb=" N LYS I 474 " --> pdb=" O LEU I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 492 through 496 Processing helix chain 'I' and resid 501 through 520 removed outlier: 3.509A pdb=" N THR I 520 " --> pdb=" O GLY I 516 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 34 Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.774A pdb=" N VAL C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 59 removed outlier: 3.866A pdb=" N GLU C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 85 removed outlier: 3.555A pdb=" N GLU C 76 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 155 through 170 Processing helix chain 'C' and resid 229 through 244 Proline residue: C 235 - end of helix removed outlier: 3.973A pdb=" N ARG C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 268 Processing helix chain 'C' and resid 283 through 295 removed outlier: 3.584A pdb=" N ASP C 287 " --> pdb=" O GLN C 283 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 290 " --> pdb=" O LYS C 286 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 338 through 358 removed outlier: 4.402A pdb=" N LEU C 354 " --> pdb=" O LYS C 350 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER C 358 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 374 removed outlier: 3.672A pdb=" N LEU C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 372 " --> pdb=" O ARG C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 410 removed outlier: 3.646A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 425 removed outlier: 3.952A pdb=" N ALA C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 448 removed outlier: 3.587A pdb=" N ARG C 448 " --> pdb=" O LYS C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.722A pdb=" N ARG C 452 " --> pdb=" O ARG C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 476 removed outlier: 4.226A pdb=" N LYS C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'C' and resid 501 through 520 removed outlier: 3.775A pdb=" N THR C 520 " --> pdb=" O GLY C 516 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 29 removed outlier: 3.627A pdb=" N ALA J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL J 29 " --> pdb=" O ASN J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 59 removed outlier: 3.602A pdb=" N GLU J 59 " --> pdb=" O THR J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 86 removed outlier: 3.681A pdb=" N GLY J 70 " --> pdb=" O TYR J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 109 Processing helix chain 'J' and resid 112 through 135 Processing helix chain 'J' and resid 140 through 152 Processing helix chain 'J' and resid 155 through 170 Processing helix chain 'J' and resid 201 through 205 Processing helix chain 'J' and resid 229 through 244 Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 255 through 269 Processing helix chain 'J' and resid 283 through 297 removed outlier: 4.028A pdb=" N ASP J 287 " --> pdb=" O GLN J 283 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU J 295 " --> pdb=" O ASP J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 352 removed outlier: 3.504A pdb=" N ILE J 342 " --> pdb=" O SER J 338 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA J 344 " --> pdb=" O GLU J 340 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG J 345 " --> pdb=" O ALA J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 356 through 360 removed outlier: 3.599A pdb=" N ASP J 359 " --> pdb=" O THR J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 361 through 373 removed outlier: 4.291A pdb=" N LYS J 371 " --> pdb=" O GLU J 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 410 Processing helix chain 'J' and resid 416 through 425 removed outlier: 4.136A pdb=" N ALA J 425 " --> pdb=" O ARG J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 448 Processing helix chain 'J' and resid 448 through 459 removed outlier: 3.875A pdb=" N ARG J 452 " --> pdb=" O ARG J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 476 removed outlier: 4.027A pdb=" N LYS J 474 " --> pdb=" O LEU J 470 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 496 Processing helix chain 'J' and resid 501 through 520 Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.777A pdb=" N VAL D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 59 removed outlier: 3.850A pdb=" N GLU D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 85 removed outlier: 3.516A pdb=" N GLU D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 109 Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 229 through 244 Proline residue: D 235 - end of helix removed outlier: 3.580A pdb=" N ARG D 242 " --> pdb=" O GLU D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 283 through 295 removed outlier: 3.552A pdb=" N ASP D 287 " --> pdb=" O GLN D 283 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN D 290 " --> pdb=" O LYS D 286 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP D 291 " --> pdb=" O ASP D 287 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 357 removed outlier: 3.760A pdb=" N ILE D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU D 354 " --> pdb=" O LYS D 350 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 374 removed outlier: 3.545A pdb=" N LEU D 369 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D 372 " --> pdb=" O ARG D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 410 removed outlier: 3.656A pdb=" N GLU D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 425 removed outlier: 3.948A pdb=" N ALA D 425 " --> pdb=" O ARG D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 429 Processing helix chain 'D' and resid 433 through 448 removed outlier: 3.594A pdb=" N ARG D 448 " --> pdb=" O LYS D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.725A pdb=" N ARG D 452 " --> pdb=" O ARG D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 476 removed outlier: 4.191A pdb=" N LYS D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'D' and resid 501 through 520 removed outlier: 3.806A pdb=" N THR D 520 " --> pdb=" O GLY D 516 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 29 removed outlier: 3.661A pdb=" N ALA K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL K 29 " --> pdb=" O ASN K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 removed outlier: 3.506A pdb=" N GLU K 59 " --> pdb=" O THR K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 86 removed outlier: 3.560A pdb=" N GLY K 70 " --> pdb=" O TYR K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 109 Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 Processing helix chain 'K' and resid 201 through 205 Processing helix chain 'K' and resid 229 through 244 Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 255 through 269 Processing helix chain 'K' and resid 283 through 296 removed outlier: 4.043A pdb=" N ASP K 287 " --> pdb=" O GLN K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 352 removed outlier: 4.590A pdb=" N ALA K 344 " --> pdb=" O GLU K 340 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ARG K 345 " --> pdb=" O ALA K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 356 through 360 removed outlier: 3.579A pdb=" N ASP K 359 " --> pdb=" O THR K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 373 removed outlier: 4.082A pdb=" N LYS K 371 " --> pdb=" O GLU K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 410 Processing helix chain 'K' and resid 416 through 424 Processing helix chain 'K' and resid 425 through 427 No H-bonds generated for 'chain 'K' and resid 425 through 427' Processing helix chain 'K' and resid 433 through 448 Processing helix chain 'K' and resid 448 through 459 removed outlier: 3.881A pdb=" N ARG K 452 " --> pdb=" O ARG K 448 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 476 removed outlier: 4.016A pdb=" N LYS K 474 " --> pdb=" O LEU K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 492 through 496 Processing helix chain 'K' and resid 501 through 520 removed outlier: 3.502A pdb=" N THR K 520 " --> pdb=" O GLY K 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 29 removed outlier: 3.786A pdb=" N VAL E 29 " --> pdb=" O ASN E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 59 removed outlier: 3.880A pdb=" N GLU E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 85 removed outlier: 3.531A pdb=" N GLU E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 109 Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 155 through 170 Processing helix chain 'E' and resid 229 through 244 Proline residue: E 235 - end of helix removed outlier: 4.306A pdb=" N ARG E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 282 through 295 removed outlier: 4.264A pdb=" N LYS E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN E 290 " --> pdb=" O LYS E 286 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 357 removed outlier: 3.906A pdb=" N ILE E 342 " --> pdb=" O SER E 338 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN E 343 " --> pdb=" O LYS E 339 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU E 354 " --> pdb=" O LYS E 350 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU E 355 " --> pdb=" O ARG E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 374 removed outlier: 3.551A pdb=" N LEU E 369 " --> pdb=" O LEU E 365 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU E 372 " --> pdb=" O ARG E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 410 removed outlier: 3.669A pdb=" N GLU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 425 removed outlier: 3.935A pdb=" N ALA E 425 " --> pdb=" O ARG E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 429 Processing helix chain 'E' and resid 433 through 448 removed outlier: 3.600A pdb=" N ARG E 448 " --> pdb=" O LYS E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.720A pdb=" N ARG E 452 " --> pdb=" O ARG E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 476 removed outlier: 4.179A pdb=" N LYS E 474 " --> pdb=" O LEU E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 496 Processing helix chain 'E' and resid 501 through 520 removed outlier: 3.759A pdb=" N THR E 520 " --> pdb=" O GLY E 516 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 29 removed outlier: 3.652A pdb=" N ALA L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 59 removed outlier: 3.601A pdb=" N GLU L 59 " --> pdb=" O THR L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 86 removed outlier: 3.678A pdb=" N GLY L 70 " --> pdb=" O TYR L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 109 Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 155 through 170 Processing helix chain 'L' and resid 201 through 205 removed outlier: 3.841A pdb=" N PHE L 204 " --> pdb=" O SER L 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 244 Proline residue: L 235 - end of helix Processing helix chain 'L' and resid 255 through 269 Processing helix chain 'L' and resid 283 through 294 removed outlier: 3.705A pdb=" N ASP L 287 " --> pdb=" O GLN L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 352 Processing helix chain 'L' and resid 356 through 360 removed outlier: 3.508A pdb=" N ASP L 359 " --> pdb=" O THR L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 361 through 373 removed outlier: 4.122A pdb=" N LYS L 371 " --> pdb=" O GLU L 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 410 Processing helix chain 'L' and resid 416 through 424 Processing helix chain 'L' and resid 425 through 427 No H-bonds generated for 'chain 'L' and resid 425 through 427' Processing helix chain 'L' and resid 433 through 448 Processing helix chain 'L' and resid 448 through 459 removed outlier: 3.880A pdb=" N ARG L 452 " --> pdb=" O ARG L 448 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 476 removed outlier: 4.034A pdb=" N LYS L 474 " --> pdb=" O LEU L 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 496 Processing helix chain 'L' and resid 501 through 520 removed outlier: 3.507A pdb=" N THR L 520 " --> pdb=" O GLY L 516 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 34 Processing helix chain 'F' and resid 9 through 29 removed outlier: 3.793A pdb=" N VAL F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 59 removed outlier: 3.884A pdb=" N GLU F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 85 removed outlier: 3.507A pdb=" N GLU F 76 " --> pdb=" O GLN F 72 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 109 Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 Processing helix chain 'F' and resid 229 through 244 Proline residue: F 235 - end of helix removed outlier: 3.702A pdb=" N ARG F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 268 Processing helix chain 'F' and resid 283 through 295 removed outlier: 3.519A pdb=" N ASP F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU F 295 " --> pdb=" O ASP F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 312 Processing helix chain 'F' and resid 338 through 357 removed outlier: 3.791A pdb=" N ILE F 342 " --> pdb=" O SER F 338 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN F 343 " --> pdb=" O LYS F 339 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG F 351 " --> pdb=" O GLU F 347 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU F 354 " --> pdb=" O LYS F 350 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 372 removed outlier: 3.976A pdb=" N LEU F 372 " --> pdb=" O ARG F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 410 removed outlier: 3.628A pdb=" N GLU F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 425 removed outlier: 3.951A pdb=" N ALA F 425 " --> pdb=" O ARG F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 448 removed outlier: 3.592A pdb=" N ARG F 448 " --> pdb=" O LYS F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.709A pdb=" N ARG F 452 " --> pdb=" O ARG F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 476 removed outlier: 4.230A pdb=" N LYS F 474 " --> pdb=" O LEU F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 496 Processing helix chain 'F' and resid 501 through 520 removed outlier: 3.772A pdb=" N THR F 520 " --> pdb=" O GLY F 516 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 29 removed outlier: 3.676A pdb=" N ALA M 26 " --> pdb=" O LYS M 22 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL M 29 " --> pdb=" O ASN M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 59 removed outlier: 3.652A pdb=" N GLU M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 86 removed outlier: 3.611A pdb=" N GLY M 70 " --> pdb=" O TYR M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 109 Processing helix chain 'M' and resid 112 through 135 Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'M' and resid 155 through 170 Processing helix chain 'M' and resid 201 through 205 removed outlier: 3.683A pdb=" N PHE M 204 " --> pdb=" O SER M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 244 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 255 through 269 Processing helix chain 'M' and resid 283 through 297 removed outlier: 3.855A pdb=" N ASP M 287 " --> pdb=" O GLN M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 310 removed outlier: 3.724A pdb=" N LEU M 309 " --> pdb=" O GLY M 306 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU M 310 " --> pdb=" O ILE M 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 306 through 310' Processing helix chain 'M' and resid 342 through 352 Processing helix chain 'M' and resid 354 through 360 removed outlier: 4.438A pdb=" N SER M 358 " --> pdb=" O GLU M 355 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP M 359 " --> pdb=" O THR M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 361 through 373 removed outlier: 4.118A pdb=" N LYS M 371 " --> pdb=" O GLU M 367 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 410 removed outlier: 3.577A pdb=" N GLU M 391 " --> pdb=" O ALA M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 424 Processing helix chain 'M' and resid 425 through 427 No H-bonds generated for 'chain 'M' and resid 425 through 427' Processing helix chain 'M' and resid 433 through 448 Processing helix chain 'M' and resid 448 through 459 removed outlier: 3.868A pdb=" N ARG M 452 " --> pdb=" O ARG M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 476 removed outlier: 4.067A pdb=" N LYS M 474 " --> pdb=" O LEU M 470 " (cutoff:3.500A) Processing helix chain 'M' and resid 492 through 496 Processing helix chain 'M' and resid 501 through 520 removed outlier: 3.517A pdb=" N THR M 520 " --> pdb=" O GLY M 516 " (cutoff:3.500A) Processing helix chain 'f' and resid 88 through 90 No H-bonds generated for 'chain 'f' and resid 88 through 90' Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.796A pdb=" N VAL G 29 " --> pdb=" O ASN G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 59 removed outlier: 3.878A pdb=" N GLU G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 85 removed outlier: 3.513A pdb=" N GLU G 76 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 109 Processing helix chain 'G' and resid 112 through 135 Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 155 through 170 Processing helix chain 'G' and resid 229 through 244 Proline residue: G 235 - end of helix removed outlier: 4.008A pdb=" N ARG G 242 " --> pdb=" O GLU G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 268 Processing helix chain 'G' and resid 283 through 295 removed outlier: 3.516A pdb=" N ASP G 291 " --> pdb=" O ASP G 287 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU G 295 " --> pdb=" O ASP G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 357 removed outlier: 3.872A pdb=" N ILE G 342 " --> pdb=" O SER G 338 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN G 343 " --> pdb=" O LYS G 339 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU G 354 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU G 355 " --> pdb=" O ARG G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 363 through 374 removed outlier: 3.642A pdb=" N LEU G 369 " --> pdb=" O LEU G 365 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU G 372 " --> pdb=" O ARG G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 410 removed outlier: 3.679A pdb=" N GLU G 391 " --> pdb=" O ALA G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 425 removed outlier: 3.952A pdb=" N ALA G 425 " --> pdb=" O ARG G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 428 No H-bonds generated for 'chain 'G' and resid 426 through 428' Processing helix chain 'G' and resid 433 through 448 removed outlier: 3.595A pdb=" N ARG G 448 " --> pdb=" O LYS G 444 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 458 removed outlier: 3.710A pdb=" N ARG G 452 " --> pdb=" O ARG G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 476 removed outlier: 4.192A pdb=" N LYS G 474 " --> pdb=" O LEU G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 496 Processing helix chain 'G' and resid 501 through 520 removed outlier: 3.796A pdb=" N THR G 520 " --> pdb=" O GLY G 516 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 29 removed outlier: 3.679A pdb=" N ALA N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL N 29 " --> pdb=" O ASN N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 59 removed outlier: 3.502A pdb=" N GLU N 59 " --> pdb=" O THR N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 86 removed outlier: 3.688A pdb=" N GLY N 70 " --> pdb=" O TYR N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 109 Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 140 through 152 Processing helix chain 'N' and resid 155 through 170 Processing helix chain 'N' and resid 201 through 205 removed outlier: 3.586A pdb=" N PHE N 204 " --> pdb=" O SER N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 242 Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 255 through 269 Processing helix chain 'N' and resid 283 through 296 removed outlier: 3.998A pdb=" N ASP N 287 " --> pdb=" O GLN N 283 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE N 292 " --> pdb=" O TYR N 288 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA N 293 " --> pdb=" O LEU N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 342 through 352 Processing helix chain 'N' and resid 356 through 360 Processing helix chain 'N' and resid 361 through 373 removed outlier: 4.089A pdb=" N LYS N 371 " --> pdb=" O GLU N 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 410 Processing helix chain 'N' and resid 416 through 424 Processing helix chain 'N' and resid 425 through 427 No H-bonds generated for 'chain 'N' and resid 425 through 427' Processing helix chain 'N' and resid 433 through 448 Processing helix chain 'N' and resid 448 through 459 removed outlier: 3.878A pdb=" N ARG N 452 " --> pdb=" O ARG N 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 461 through 476 removed outlier: 4.023A pdb=" N LYS N 474 " --> pdb=" O LEU N 470 " (cutoff:3.500A) Processing helix chain 'N' and resid 492 through 496 Processing helix chain 'N' and resid 501 through 520 removed outlier: 3.518A pdb=" N THR N 520 " --> pdb=" O GLY N 516 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 7.393A pdb=" N ILE G 39 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU A 524 " --> pdb=" O ILE G 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 7.510A pdb=" N GLU A 37 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU B 524 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 39 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ALA B 526 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.437A pdb=" N VAL A 174 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE A 379 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR A 176 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL A 381 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU A 178 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.648A pdb=" N LEU A 247 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 220 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY A 318 " --> pdb=" O ILE A 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA8, first strand: chain 'A' and resid 480 through 483 Processing sheet with id=AA9, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.237A pdb=" N GLU I 37 " --> pdb=" O ALA H 521 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA H 523 " --> pdb=" O GLU I 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 48 through 50 removed outlier: 7.119A pdb=" N GLU H 37 " --> pdb=" O ALA N 523 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N VAL N 525 " --> pdb=" O GLU H 37 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE H 39 " --> pdb=" O VAL N 525 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N GLU N 527 " --> pdb=" O ILE H 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 175 through 178 removed outlier: 6.675A pdb=" N THR H 176 " --> pdb=" O ILE H 379 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.447A pdb=" N LYS H 322 " --> pdb=" O VAL H 333 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL H 323 " --> pdb=" O LEU H 215 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU H 215 " --> pdb=" O VAL H 323 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 219 through 222 removed outlier: 6.506A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AB6, first strand: chain 'H' and resid 480 through 483 removed outlier: 3.883A pdb=" N ASP H 488 " --> pdb=" O ASP H 483 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'a' and resid 5 through 6 removed outlier: 6.475A pdb=" N VAL b 12 " --> pdb=" O ILE b 43 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL b 45 " --> pdb=" O LYS b 10 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LYS b 10 " --> pdb=" O VAL b 45 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ARG b 15 " --> pdb=" O LYS b 83 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N LYS b 83 " --> pdb=" O ARG b 15 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'a' and resid 75 through 79 removed outlier: 9.764A pdb=" N LYS a 83 " --> pdb=" O ARG a 15 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG a 15 " --> pdb=" O LYS a 83 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS a 10 " --> pdb=" O VAL a 45 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL a 45 " --> pdb=" O LYS a 10 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL a 12 " --> pdb=" O ILE a 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'a' and resid 21 through 22 removed outlier: 4.120A pdb=" N GLN a 21 " --> pdb=" O ILE a 29 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 49 through 50 Processing sheet with id=AC2, first strand: chain 'h' and resid 42 through 45 removed outlier: 7.371A pdb=" N VAL h 12 " --> pdb=" O ILE h 43 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL h 45 " --> pdb=" O LYS h 10 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LYS h 10 " --> pdb=" O VAL h 45 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 50 removed outlier: 7.498A pdb=" N GLU B 37 " --> pdb=" O GLU C 522 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU C 524 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE B 39 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ALA C 526 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 174 through 179 removed outlier: 3.629A pdb=" N VAL B 174 " --> pdb=" O GLY B 375 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 194 through 195 Processing sheet with id=AC6, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.575A pdb=" N LEU B 247 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 220 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 318 " --> pdb=" O ILE B 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AC8, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AC9, first strand: chain 'B' and resid 480 through 483 Processing sheet with id=AD1, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.233A pdb=" N GLU J 37 " --> pdb=" O ALA I 521 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA I 523 " --> pdb=" O GLU J 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 175 through 178 removed outlier: 6.625A pdb=" N THR I 176 " --> pdb=" O ILE I 379 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 219 through 222 Processing sheet with id=AD4, first strand: chain 'I' and resid 320 through 325 removed outlier: 6.767A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS I 322 " --> pdb=" O VAL I 333 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AD6, first strand: chain 'I' and resid 480 through 483 removed outlier: 3.891A pdb=" N ASP I 488 " --> pdb=" O ASP I 483 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'b' and resid 5 through 6 removed outlier: 3.504A pdb=" N VAL c 95 " --> pdb=" O ARG b 5 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL c 12 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL c 45 " --> pdb=" O LYS c 10 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LYS c 10 " --> pdb=" O VAL c 45 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG c 15 " --> pdb=" O LYS c 83 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N LYS c 83 " --> pdb=" O ARG c 15 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'b' and resid 21 through 22 removed outlier: 4.147A pdb=" N GLN b 21 " --> pdb=" O ILE b 29 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'i' and resid 42 through 45 removed outlier: 6.981A pdb=" N VAL i 12 " --> pdb=" O ILE i 43 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL i 45 " --> pdb=" O LYS i 10 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LYS i 10 " --> pdb=" O VAL i 45 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 50 removed outlier: 7.521A pdb=" N GLU C 37 " --> pdb=" O GLU D 522 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU D 524 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE C 39 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ALA D 526 " --> pdb=" O ILE C 39 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 174 through 179 removed outlier: 3.619A pdb=" N VAL C 174 " --> pdb=" O GLY C 375 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 213 through 216 Processing sheet with id=AE4, first strand: chain 'C' and resid 273 through 277 removed outlier: 3.503A pdb=" N ALA C 251 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 220 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY C 318 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 226 through 227 Processing sheet with id=AE6, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AE7, first strand: chain 'C' and resid 480 through 483 Processing sheet with id=AE8, first strand: chain 'J' and resid 4 through 8 removed outlier: 6.238A pdb=" N GLU K 37 " --> pdb=" O ALA J 521 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA J 523 " --> pdb=" O GLU K 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 175 through 178 removed outlier: 6.640A pdb=" N THR J 176 " --> pdb=" O ILE J 379 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 193 through 195 removed outlier: 6.594A pdb=" N LYS J 322 " --> pdb=" O VAL J 333 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 219 through 222 removed outlier: 6.593A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AF4, first strand: chain 'J' and resid 480 through 483 removed outlier: 3.850A pdb=" N ASP J 488 " --> pdb=" O ASP J 483 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'c' and resid 5 through 6 removed outlier: 6.586A pdb=" N VAL d 12 " --> pdb=" O ILE d 43 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL d 45 " --> pdb=" O LYS d 10 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS d 10 " --> pdb=" O VAL d 45 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG d 15 " --> pdb=" O LYS d 83 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N LYS d 83 " --> pdb=" O ARG d 15 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'c' and resid 21 through 22 removed outlier: 4.430A pdb=" N GLN c 21 " --> pdb=" O ILE c 29 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'c' and resid 49 through 50 Processing sheet with id=AF8, first strand: chain 'j' and resid 42 through 45 removed outlier: 7.430A pdb=" N VAL j 12 " --> pdb=" O ILE j 43 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL j 45 " --> pdb=" O LYS j 10 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LYS j 10 " --> pdb=" O VAL j 45 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE j 86 " --> pdb=" O THR j 75 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR j 75 " --> pdb=" O ILE j 86 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 48 through 50 removed outlier: 7.532A pdb=" N GLU D 37 " --> pdb=" O GLU E 522 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU E 524 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE D 39 " --> pdb=" O LEU E 524 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ALA E 526 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 174 through 179 removed outlier: 6.409A pdb=" N VAL D 174 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE D 379 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR D 176 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL D 381 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU D 178 " --> pdb=" O VAL D 381 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 213 through 216 Processing sheet with id=AG3, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.470A pdb=" N LEU D 247 " --> pdb=" O CYS D 274 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL D 276 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE D 249 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE D 220 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY D 318 " --> pdb=" O ILE D 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'D' and resid 226 through 227 Processing sheet with id=AG5, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AG6, first strand: chain 'D' and resid 480 through 483 Processing sheet with id=AG7, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.243A pdb=" N GLU L 37 " --> pdb=" O ALA K 521 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA K 523 " --> pdb=" O GLU L 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 175 through 178 removed outlier: 6.420A pdb=" N THR K 176 " --> pdb=" O ILE K 379 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 219 through 222 removed outlier: 6.383A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'K' and resid 320 through 325 removed outlier: 6.884A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS K 322 " --> pdb=" O VAL K 333 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AH3, first strand: chain 'K' and resid 480 through 483 removed outlier: 3.875A pdb=" N ASP K 488 " --> pdb=" O ASP K 483 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'd' and resid 5 through 6 removed outlier: 6.518A pdb=" N VAL e 12 " --> pdb=" O ILE e 43 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL e 45 " --> pdb=" O LYS e 10 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LYS e 10 " --> pdb=" O VAL e 45 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ARG e 15 " --> pdb=" O LYS e 83 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N LYS e 83 " --> pdb=" O ARG e 15 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'd' and resid 21 through 22 removed outlier: 4.217A pdb=" N GLN d 21 " --> pdb=" O ILE d 29 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'd' and resid 49 through 50 Processing sheet with id=AH7, first strand: chain 'k' and resid 42 through 45 removed outlier: 7.180A pdb=" N VAL k 12 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL k 45 " --> pdb=" O LYS k 10 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LYS k 10 " --> pdb=" O VAL k 45 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU k 85 " --> pdb=" O VAL k 13 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE k 86 " --> pdb=" O THR k 75 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR k 75 " --> pdb=" O ILE k 86 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 48 through 50 removed outlier: 7.557A pdb=" N GLU E 37 " --> pdb=" O GLU F 522 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU F 524 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE E 39 " --> pdb=" O LEU F 524 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ALA F 526 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 174 through 179 removed outlier: 3.596A pdb=" N VAL E 174 " --> pdb=" O GLY E 375 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 194 through 195 removed outlier: 3.519A pdb=" N VAL E 323 " --> pdb=" O LEU E 215 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 273 through 277 removed outlier: 6.667A pdb=" N LEU E 247 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL E 276 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE E 249 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 220 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY E 318 " --> pdb=" O ILE E 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'E' and resid 226 through 227 Processing sheet with id=AI4, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AI5, first strand: chain 'E' and resid 480 through 483 Processing sheet with id=AI6, first strand: chain 'L' and resid 4 through 8 removed outlier: 6.224A pdb=" N GLU M 37 " --> pdb=" O ALA L 521 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA L 523 " --> pdb=" O GLU M 37 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 175 through 178 removed outlier: 6.736A pdb=" N THR L 176 " --> pdb=" O ILE L 379 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 193 through 195 removed outlier: 3.507A pdb=" N MET L 193 " --> pdb=" O ILE L 332 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS L 322 " --> pdb=" O VAL L 333 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 219 through 222 removed outlier: 6.650A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI9 Processing sheet with id=AJ1, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AJ2, first strand: chain 'L' and resid 480 through 483 removed outlier: 3.855A pdb=" N ASP L 488 " --> pdb=" O ASP L 483 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'e' and resid 5 through 6 removed outlier: 6.600A pdb=" N VAL f 12 " --> pdb=" O ILE f 43 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG f 15 " --> pdb=" O LYS f 83 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N LYS f 83 " --> pdb=" O ARG f 15 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'e' and resid 21 through 22 removed outlier: 4.344A pdb=" N GLN e 21 " --> pdb=" O ILE e 29 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'e' and resid 49 through 50 Processing sheet with id=AJ6, first strand: chain 'l' and resid 42 through 45 removed outlier: 7.173A pdb=" N VAL l 12 " --> pdb=" O ILE l 43 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL l 45 " --> pdb=" O LYS l 10 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS l 10 " --> pdb=" O VAL l 45 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'l' and resid 49 through 50 Processing sheet with id=AJ8, first strand: chain 'F' and resid 48 through 50 removed outlier: 7.521A pdb=" N GLU F 37 " --> pdb=" O GLU G 522 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU G 524 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE F 39 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ALA G 526 " --> pdb=" O ILE F 39 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 174 through 179 removed outlier: 6.445A pdb=" N VAL F 174 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE F 379 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR F 176 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL F 381 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU F 178 " --> pdb=" O VAL F 381 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'F' and resid 213 through 216 Processing sheet with id=AK2, first strand: chain 'F' and resid 219 through 222 removed outlier: 6.267A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU F 247 " --> pdb=" O CYS F 274 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK2 Processing sheet with id=AK3, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AK4, first strand: chain 'F' and resid 480 through 483 Processing sheet with id=AK5, first strand: chain 'M' and resid 4 through 8 removed outlier: 6.242A pdb=" N GLU N 37 " --> pdb=" O ALA M 521 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA M 523 " --> pdb=" O GLU N 37 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'M' and resid 175 through 178 removed outlier: 6.671A pdb=" N THR M 176 " --> pdb=" O ILE M 379 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'M' and resid 193 through 195 removed outlier: 6.581A pdb=" N LYS M 322 " --> pdb=" O VAL M 333 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'M' and resid 219 through 222 removed outlier: 3.605A pdb=" N LEU M 248 " --> pdb=" O PHE M 219 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AL1, first strand: chain 'M' and resid 480 through 483 removed outlier: 3.896A pdb=" N ASP M 488 " --> pdb=" O ASP M 483 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'f' and resid 5 through 6 removed outlier: 6.890A pdb=" N VAL g 12 " --> pdb=" O ILE g 43 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL g 45 " --> pdb=" O LYS g 10 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LYS g 10 " --> pdb=" O VAL g 45 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ARG g 15 " --> pdb=" O LYS g 83 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N LYS g 83 " --> pdb=" O ARG g 15 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'f' and resid 21 through 22 removed outlier: 4.294A pdb=" N GLN f 21 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'f' and resid 49 through 50 Processing sheet with id=AL5, first strand: chain 'm' and resid 42 through 45 removed outlier: 7.024A pdb=" N VAL m 12 " --> pdb=" O ILE m 43 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL m 45 " --> pdb=" O LYS m 10 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LYS m 10 " --> pdb=" O VAL m 45 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'G' and resid 174 through 179 removed outlier: 6.440A pdb=" N VAL G 174 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE G 379 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR G 176 " --> pdb=" O ILE G 379 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL G 381 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU G 178 " --> pdb=" O VAL G 381 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'G' and resid 194 through 195 removed outlier: 3.504A pdb=" N VAL G 323 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'G' and resid 273 through 277 removed outlier: 6.534A pdb=" N LEU G 247 " --> pdb=" O CYS G 274 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL G 276 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE G 249 " --> pdb=" O VAL G 276 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE G 220 " --> pdb=" O GLY G 318 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY G 318 " --> pdb=" O ILE G 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL8 Processing sheet with id=AL9, first strand: chain 'G' and resid 226 through 227 Processing sheet with id=AM1, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AM2, first strand: chain 'G' and resid 480 through 483 Processing sheet with id=AM3, first strand: chain 'N' and resid 175 through 178 removed outlier: 6.563A pdb=" N THR N 176 " --> pdb=" O ILE N 379 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'N' and resid 193 through 194 removed outlier: 6.699A pdb=" N LYS N 322 " --> pdb=" O VAL N 333 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY N 335 " --> pdb=" O ALA N 320 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA N 320 " --> pdb=" O GLY N 335 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'N' and resid 219 through 222 Processing sheet with id=AM6, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AM7, first strand: chain 'N' and resid 480 through 483 removed outlier: 3.894A pdb=" N ASP N 488 " --> pdb=" O ASP N 483 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'g' and resid 21 through 22 removed outlier: 4.281A pdb=" N GLN g 21 " --> pdb=" O ILE g 29 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'g' and resid 49 through 50 Processing sheet with id=AN1, first strand: chain 'n' and resid 42 through 45 removed outlier: 3.872A pdb=" N ALA n 44 " --> pdb=" O VAL n 12 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR n 75 " --> pdb=" O ILE n 86 " (cutoff:3.500A) 3532 hydrogen bonds defined for protein. 10221 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: 31.41 Time building geometry restraints manager: 15.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 21897 1.34 - 1.46: 11690 1.46 - 1.58: 31492 1.58 - 1.70: 56 1.70 - 1.82: 322 Bond restraints: 65457 Sorted by residual: bond pdb=" CB LYS B 327 " pdb=" CG LYS B 327 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" CB LYS G 327 " pdb=" CG LYS G 327 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" CB LYS A 327 " pdb=" CG LYS A 327 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CB LYS D 327 " pdb=" CG LYS D 327 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CB LYS C 327 " pdb=" CG LYS C 327 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.65e+00 ... (remaining 65452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 87994 3.38 - 6.75: 341 6.75 - 10.13: 52 10.13 - 13.51: 8 13.51 - 16.89: 1 Bond angle restraints: 88396 Sorted by residual: angle pdb=" CB MET L 211 " pdb=" CG MET L 211 " pdb=" SD MET L 211 " ideal model delta sigma weight residual 112.70 129.59 -16.89 3.00e+00 1.11e-01 3.17e+01 angle pdb=" C TYR f 8 " pdb=" CA TYR f 8 " pdb=" CB TYR f 8 " ideal model delta sigma weight residual 117.23 110.11 7.12 1.36e+00 5.41e-01 2.74e+01 angle pdb=" N MET L 211 " pdb=" CA MET L 211 " pdb=" C MET L 211 " ideal model delta sigma weight residual 110.91 105.53 5.38 1.17e+00 7.31e-01 2.11e+01 angle pdb=" CB LYS G 327 " pdb=" CG LYS G 327 " pdb=" CD LYS G 327 " ideal model delta sigma weight residual 111.30 121.36 -10.06 2.30e+00 1.89e-01 1.91e+01 angle pdb=" CB LYS A 327 " pdb=" CG LYS A 327 " pdb=" CD LYS A 327 " ideal model delta sigma weight residual 111.30 121.32 -10.02 2.30e+00 1.89e-01 1.90e+01 ... (remaining 88391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 36077 17.99 - 35.98: 3415 35.98 - 53.97: 881 53.97 - 71.96: 280 71.96 - 89.95: 199 Dihedral angle restraints: 40852 sinusoidal: 16597 harmonic: 24255 Sorted by residual: dihedral pdb=" CA MET d 16 " pdb=" C MET d 16 " pdb=" N GLU d 17 " pdb=" CA GLU d 17 " ideal model delta harmonic sigma weight residual -180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA MET e 16 " pdb=" C MET e 16 " pdb=" N GLU e 17 " pdb=" CA GLU e 17 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA TYR G 223 " pdb=" C TYR G 223 " pdb=" N GLU G 224 " pdb=" CA GLU G 224 " ideal model delta harmonic sigma weight residual -180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 40849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 6865 0.031 - 0.062: 2310 0.062 - 0.094: 815 0.094 - 0.125: 541 0.125 - 0.156: 67 Chirality restraints: 10598 Sorted by residual: chirality pdb=" CA ASP e 80 " pdb=" N ASP e 80 " pdb=" C ASP e 80 " pdb=" CB ASP e 80 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.07e-01 chirality pdb=" CG LEU C 314 " pdb=" CB LEU C 314 " pdb=" CD1 LEU C 314 " pdb=" CD2 LEU C 314 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ILE J 250 " pdb=" N ILE J 250 " pdb=" C ILE J 250 " pdb=" CB ILE J 250 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 10595 not shown) Planarity restraints: 11312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 44 " 0.016 2.00e-02 2.50e+03 1.62e-02 6.59e+00 pdb=" CG TRP E 44 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP E 44 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP E 44 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 44 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 44 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 44 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 44 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 44 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 44 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 44 " -0.013 2.00e-02 2.50e+03 1.38e-02 4.79e+00 pdb=" CG TRP A 44 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 44 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 44 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 44 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 44 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 44 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 44 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 44 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 44 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET L 211 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" C MET L 211 " 0.035 2.00e-02 2.50e+03 pdb=" O MET L 211 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU L 212 " -0.012 2.00e-02 2.50e+03 ... (remaining 11309 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.63: 675 2.63 - 3.26: 68605 3.26 - 3.89: 128177 3.89 - 4.51: 170747 4.51 - 5.14: 263659 Nonbonded interactions: 631863 Sorted by model distance: nonbonded pdb=" OD1 ASP H 87 " pdb="MG MG H 601 " model vdw 2.007 2.170 nonbonded pdb=" OD1 ASP J 87 " pdb="MG MG J 601 " model vdw 2.009 2.170 nonbonded pdb=" OD1 ASP N 87 " pdb="MG MG N 601 " model vdw 2.009 2.170 nonbonded pdb=" OD1 ASP L 87 " pdb="MG MG L 601 " model vdw 2.010 2.170 nonbonded pdb=" OD1 ASP M 87 " pdb="MG MG M 601 " model vdw 2.016 2.170 ... (remaining 631858 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 3 through 529 or resid 602)) selection = (chain 'B' and (resid 3 through 529 or resid 602)) selection = (chain 'C' and (resid 3 through 529 or resid 602)) selection = (chain 'D' and (resid 3 through 529 or resid 602)) selection = (chain 'E' and (resid 3 through 529 or resid 602)) selection = (chain 'F' and (resid 3 through 529 or resid 602)) selection = (chain 'G' and (resid 3 through 529 or resid 602)) selection = (chain 'H' and (resid 3 through 529 or resid 603)) selection = (chain 'I' and (resid 3 through 529 or resid 603)) selection = (chain 'J' and (resid 3 through 529 or resid 603)) selection = (chain 'K' and (resid 3 through 529 or resid 603)) selection = (chain 'L' and (resid 3 through 529 or resid 603)) selection = (chain 'M' and (resid 3 through 529 or resid 603)) selection = (chain 'N' and (resid 3 through 529 or resid 603)) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' } 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: 10.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 2.310 Check model and map are aligned: 0.390 Set scattering table: 0.480 Process input model: 127.100 Find NCS groups from input model: 3.570 Set up NCS constraints: 0.640 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: 0.020 Load rotamer database and sin/cos tables:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.002 0.040 65457 Z= 0.141 Angle : 0.580 16.886 88396 Z= 0.294 Chirality : 0.042 0.156 10598 Planarity : 0.003 0.053 11312 Dihedral : 17.053 89.948 25270 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.18 % Allowed : 18.19 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.09), residues: 8470 helix: 1.75 (0.08), residues: 3892 sheet: 1.21 (0.16), residues: 1085 loop : -0.10 (0.10), residues: 3493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP E 44 HIS 0.002 0.000 HIS F 266 PHE 0.024 0.001 PHE m 69 TYR 0.023 0.001 TYR D 223 ARG 0.014 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 554 time to evaluate : 5.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 38 GLN cc_start: 0.7779 (mt0) cc_final: 0.7443 (mm-40) REVERT: a 70 ASN cc_start: 0.8036 (t0) cc_final: 0.7607 (t0) REVERT: b 38 GLN cc_start: 0.7399 (mt0) cc_final: 0.7119 (mm-40) REVERT: b 41 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8165 (tp30) REVERT: i 8 TYR cc_start: 0.4607 (p90) cc_final: 0.4368 (p90) REVERT: i 11 ILE cc_start: 0.2931 (mm) cc_final: 0.2703 (mt) REVERT: c 41 GLU cc_start: 0.8411 (tp30) cc_final: 0.8097 (tp30) REVERT: D 288 TYR cc_start: 0.9146 (m-80) cc_final: 0.8700 (m-10) REVERT: E 316 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.6910 (pmm) REVERT: l 8 TYR cc_start: 0.4859 (p90) cc_final: 0.4579 (p90) REVERT: F 265 ASN cc_start: 0.9219 (t0) cc_final: 0.8868 (t0) REVERT: F 277 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7218 (mppt) REVERT: G 199 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6159 (t80) REVERT: G 219 PHE cc_start: 0.8558 (m-80) cc_final: 0.8329 (m-80) REVERT: G 265 ASN cc_start: 0.9219 (t0) cc_final: 0.8815 (t0) outliers start: 81 outliers final: 65 residues processed: 623 average time/residue: 1.1872 time to fit residues: 1001.8461 Evaluate side-chains 560 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 493 time to evaluate : 5.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 195 PHE Chi-restraints excluded: chain d residue 95 VAL Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 378 ILE Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 285 ARG Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 486 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 207 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 709 optimal weight: 30.0000 chunk 636 optimal weight: 0.9990 chunk 353 optimal weight: 8.9990 chunk 217 optimal weight: 5.9990 chunk 429 optimal weight: 0.0000 chunk 340 optimal weight: 0.4980 chunk 658 optimal weight: 0.6980 chunk 254 optimal weight: 0.9990 chunk 400 optimal weight: 6.9990 chunk 490 optimal weight: 1.9990 chunk 762 optimal weight: 3.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 510 ASN h 55 GLN i 55 GLN ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 38 GLN e 70 ASN l 38 GLN f 55 GLN m 55 GLN N 207 ASN g 55 GLN g 70 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 65457 Z= 0.169 Angle : 0.588 12.030 88396 Z= 0.302 Chirality : 0.044 0.158 10598 Planarity : 0.004 0.043 11312 Dihedral : 10.494 71.591 9577 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.10 % Allowed : 17.59 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.09), residues: 8470 helix: 1.88 (0.08), residues: 4081 sheet: 1.17 (0.17), residues: 980 loop : -0.12 (0.10), residues: 3409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 44 HIS 0.003 0.000 HIS H 266 PHE 0.012 0.001 PHE A 195 TYR 0.021 0.001 TYR B 223 ARG 0.013 0.000 ARG n 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 520 time to evaluate : 5.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9168 (tpt) cc_final: 0.8961 (tpp) REVERT: A 199 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.6124 (t80) REVERT: A 268 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8722 (tppt) REVERT: A 327 LYS cc_start: 0.8891 (tppt) cc_final: 0.8565 (tppt) REVERT: H 316 MET cc_start: -0.0783 (tpt) cc_final: -0.2000 (tpp) REVERT: a 38 GLN cc_start: 0.7831 (mt0) cc_final: 0.7330 (mm-40) REVERT: a 70 ASN cc_start: 0.7946 (t0) cc_final: 0.7619 (t0) REVERT: B 193 MET cc_start: 0.8452 (tpt) cc_final: 0.8016 (tpt) REVERT: b 38 GLN cc_start: 0.7458 (mt0) cc_final: 0.7140 (mm-40) REVERT: i 8 TYR cc_start: 0.4606 (p90) cc_final: 0.4368 (p90) REVERT: i 50 LEU cc_start: 0.5087 (OUTLIER) cc_final: 0.4836 (tp) REVERT: C 199 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6189 (t80) REVERT: C 265 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8819 (t0) REVERT: C 277 LYS cc_start: 0.7600 (mppt) cc_final: 0.7379 (mppt) REVERT: C 316 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7311 (pmm) REVERT: C 327 LYS cc_start: 0.8838 (tppt) cc_final: 0.8464 (tppt) REVERT: J 301 ILE cc_start: 0.0943 (OUTLIER) cc_final: 0.0725 (mt) REVERT: J 345 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8189 (tmt-80) REVERT: c 41 GLU cc_start: 0.7933 (tp30) cc_final: 0.7628 (tp30) REVERT: j 1 MET cc_start: 0.4145 (tmm) cc_final: 0.3937 (tmt) REVERT: D 199 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.5994 (t80) REVERT: D 327 LYS cc_start: 0.8887 (tppt) cc_final: 0.8574 (tppt) REVERT: D 391 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7431 (tm-30) REVERT: K 494 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: E 199 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.6339 (t80) REVERT: E 327 LYS cc_start: 0.8865 (tppt) cc_final: 0.8660 (tppt) REVERT: F 199 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.5784 (t80) REVERT: F 223 TYR cc_start: 0.8729 (t80) cc_final: 0.8476 (t80) REVERT: F 265 ASN cc_start: 0.9136 (t0) cc_final: 0.8794 (t0) REVERT: F 316 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.6906 (pmm) REVERT: F 350 LYS cc_start: 0.8153 (pptt) cc_final: 0.7780 (pptt) REVERT: F 391 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: M 314 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6740 (pp) REVERT: f 12 VAL cc_start: 0.7873 (OUTLIER) cc_final: 0.7661 (t) REVERT: G 219 PHE cc_start: 0.8841 (m-80) cc_final: 0.8555 (m-80) REVERT: G 265 ASN cc_start: 0.9181 (t0) cc_final: 0.8745 (t0) REVERT: G 285 ARG cc_start: 0.8692 (mmm-85) cc_final: 0.8082 (mmm-85) REVERT: G 316 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7375 (pmm) REVERT: N 314 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6162 (pp) REVERT: n 51 LEU cc_start: 0.1744 (OUTLIER) cc_final: 0.1250 (tp) outliers start: 212 outliers final: 67 residues processed: 674 average time/residue: 1.1901 time to fit residues: 1088.7479 Evaluate side-chains 569 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 482 time to evaluate : 5.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 301 ILE Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain J residue 345 ARG Chi-restraints excluded: chain c residue 16 MET Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 52 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 494 GLU Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain l residue 77 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 211 MET Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 423 optimal weight: 5.9990 chunk 236 optimal weight: 0.0170 chunk 634 optimal weight: 5.9990 chunk 519 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 764 optimal weight: 4.9990 chunk 825 optimal weight: 30.0000 chunk 680 optimal weight: 0.0470 chunk 757 optimal weight: 10.0000 chunk 260 optimal weight: 0.2980 chunk 613 optimal weight: 4.9990 overall best weight: 2.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** c 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 70 ASN N 207 ASN g 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 65457 Z= 0.256 Angle : 0.578 11.596 88396 Z= 0.294 Chirality : 0.044 0.171 10598 Planarity : 0.003 0.039 11312 Dihedral : 9.908 66.390 9525 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.51 % Allowed : 17.91 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.09), residues: 8470 helix: 1.92 (0.08), residues: 4074 sheet: 0.95 (0.17), residues: 966 loop : -0.13 (0.10), residues: 3430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 44 HIS 0.001 0.000 HIS N 266 PHE 0.013 0.001 PHE m 69 TYR 0.011 0.001 TYR I 66 ARG 0.008 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 502 time to evaluate : 5.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9165 (tpt) cc_final: 0.8930 (tpp) REVERT: A 199 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.5992 (t80) REVERT: A 252 GLU cc_start: 0.8423 (tt0) cc_final: 0.8040 (tt0) REVERT: A 265 ASN cc_start: 0.9077 (t0) cc_final: 0.8857 (t0) REVERT: A 268 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8701 (tppt) REVERT: A 285 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.8130 (mmm-85) REVERT: A 327 LYS cc_start: 0.8925 (tppt) cc_final: 0.8559 (tppt) REVERT: H 301 ILE cc_start: 0.1528 (OUTLIER) cc_final: 0.1243 (mt) REVERT: H 316 MET cc_start: -0.0807 (tpt) cc_final: -0.1462 (tpp) REVERT: a 38 GLN cc_start: 0.7826 (mt0) cc_final: 0.7398 (mm-40) REVERT: h 42 VAL cc_start: -0.0069 (OUTLIER) cc_final: -0.0314 (t) REVERT: B 193 MET cc_start: 0.8506 (tpt) cc_final: 0.8098 (tpt) REVERT: B 319 ARG cc_start: 0.8718 (mmm-85) cc_final: 0.7725 (tmm160) REVERT: B 478 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8560 (mmtp) REVERT: b 16 MET cc_start: 0.8139 (tpp) cc_final: 0.7730 (ttm) REVERT: b 38 GLN cc_start: 0.7461 (mt0) cc_final: 0.7260 (mt0) REVERT: i 1 MET cc_start: 0.3739 (tmm) cc_final: 0.3225 (ppp) REVERT: i 8 TYR cc_start: 0.4591 (p90) cc_final: 0.4306 (p90) REVERT: i 50 LEU cc_start: 0.5056 (OUTLIER) cc_final: 0.4815 (tp) REVERT: C 199 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6020 (t80) REVERT: C 265 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8847 (t0) REVERT: C 316 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7392 (pmm) REVERT: C 327 LYS cc_start: 0.8827 (tppt) cc_final: 0.8376 (tppt) REVERT: J 345 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8183 (tmt-80) REVERT: c 72 TYR cc_start: 0.8704 (m-10) cc_final: 0.8485 (m-10) REVERT: j 51 LEU cc_start: 0.1375 (OUTLIER) cc_final: 0.1025 (tp) REVERT: D 193 MET cc_start: 0.8392 (tpt) cc_final: 0.7992 (tpt) REVERT: D 199 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.5775 (t80) REVERT: D 327 LYS cc_start: 0.8878 (tppt) cc_final: 0.8491 (tppt) REVERT: D 391 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: K 314 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6011 (OUTLIER) REVERT: E 199 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6234 (t80) REVERT: E 316 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7378 (pmm) REVERT: E 327 LYS cc_start: 0.8876 (tppt) cc_final: 0.8540 (tppt) REVERT: e 84 TYR cc_start: 0.7155 (m-80) cc_final: 0.6930 (m-80) REVERT: F 199 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.5908 (t80) REVERT: F 223 TYR cc_start: 0.8724 (t80) cc_final: 0.8402 (t80) REVERT: F 265 ASN cc_start: 0.9131 (t0) cc_final: 0.8742 (t0) REVERT: F 316 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7231 (pmm) REVERT: F 319 ARG cc_start: 0.8697 (mmm-85) cc_final: 0.7566 (tmm160) REVERT: F 327 LYS cc_start: 0.8879 (tppt) cc_final: 0.8583 (tppt) REVERT: F 391 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: F 445 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8971 (tttm) REVERT: M 178 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8496 (mm-30) REVERT: M 314 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6751 (pp) REVERT: G 219 PHE cc_start: 0.8940 (m-80) cc_final: 0.8608 (m-80) REVERT: G 265 ASN cc_start: 0.9184 (t0) cc_final: 0.8736 (t0) REVERT: G 285 ARG cc_start: 0.8746 (mmm-85) cc_final: 0.8135 (mmm-85) REVERT: G 316 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7733 (pmm) REVERT: N 314 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.5840 (pp) REVERT: N 389 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8213 (tm) REVERT: n 51 LEU cc_start: 0.1800 (OUTLIER) cc_final: 0.1321 (tp) outliers start: 240 outliers final: 99 residues processed: 684 average time/residue: 1.1881 time to fit residues: 1106.8040 Evaluate side-chains 593 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 470 time to evaluate : 5.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 305 LEU Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 67 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain b residue 9 ASP Chi-restraints excluded: chain b residue 96 ILE Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain J residue 345 ARG Chi-restraints excluded: chain c residue 9 ASP Chi-restraints excluded: chain c residue 16 MET Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain j residue 12 VAL Chi-restraints excluded: chain j residue 51 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain k residue 68 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain l residue 77 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 445 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 301 ILE Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 755 optimal weight: 5.9990 chunk 574 optimal weight: 0.9990 chunk 396 optimal weight: 20.0000 chunk 84 optimal weight: 0.0010 chunk 364 optimal weight: 0.9980 chunk 513 optimal weight: 10.0000 chunk 766 optimal weight: 1.9990 chunk 811 optimal weight: 4.9990 chunk 400 optimal weight: 3.9990 chunk 726 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN C 348 GLN ** c 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 70 ASN N 290 GLN g 70 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 65457 Z= 0.163 Angle : 0.552 9.811 88396 Z= 0.279 Chirality : 0.044 0.303 10598 Planarity : 0.003 0.048 11312 Dihedral : 9.051 59.656 9521 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.28 % Allowed : 18.48 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.09), residues: 8470 helix: 2.00 (0.08), residues: 4074 sheet: 0.70 (0.16), residues: 1015 loop : -0.17 (0.10), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 44 HIS 0.001 0.000 HIS N 266 PHE 0.010 0.001 PHE A 195 TYR 0.011 0.001 TYR K 66 ARG 0.010 0.000 ARG a 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 492 time to evaluate : 6.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9087 (tpt) cc_final: 0.8886 (tpp) REVERT: A 199 TYR cc_start: 0.6981 (OUTLIER) cc_final: 0.5927 (t80) REVERT: A 252 GLU cc_start: 0.8417 (tt0) cc_final: 0.8058 (tt0) REVERT: A 265 ASN cc_start: 0.9106 (OUTLIER) cc_final: 0.8864 (t0) REVERT: A 268 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8682 (tppt) REVERT: A 327 LYS cc_start: 0.8895 (tppt) cc_final: 0.8531 (tppt) REVERT: A 391 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: H 301 ILE cc_start: 0.1443 (OUTLIER) cc_final: 0.0878 (mt) REVERT: H 316 MET cc_start: -0.1114 (tpt) cc_final: -0.1764 (tpp) REVERT: a 5 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7655 (ttp80) REVERT: a 38 GLN cc_start: 0.7852 (mt0) cc_final: 0.7393 (mm-40) REVERT: h 42 VAL cc_start: -0.0211 (OUTLIER) cc_final: -0.0441 (t) REVERT: B 193 MET cc_start: 0.8551 (tpt) cc_final: 0.7988 (tpt) REVERT: b 16 MET cc_start: 0.7997 (tpp) cc_final: 0.7670 (ttm) REVERT: b 38 GLN cc_start: 0.7460 (mt0) cc_final: 0.7233 (mt0) REVERT: C 199 TYR cc_start: 0.7018 (OUTLIER) cc_final: 0.6509 (t80) REVERT: C 265 ASN cc_start: 0.9120 (t0) cc_final: 0.8807 (t0) REVERT: C 277 LYS cc_start: 0.7780 (mppt) cc_final: 0.7510 (mppt) REVERT: C 316 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7307 (pmm) REVERT: J 214 VAL cc_start: 0.5803 (OUTLIER) cc_final: 0.5602 (t) REVERT: J 345 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8204 (tmt-80) REVERT: c 5 ARG cc_start: 0.8261 (ttp80) cc_final: 0.8026 (ttp80) REVERT: j 51 LEU cc_start: 0.1256 (OUTLIER) cc_final: 0.0904 (tp) REVERT: D 199 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.5420 (t80) REVERT: D 327 LYS cc_start: 0.8880 (tppt) cc_final: 0.8463 (tppt) REVERT: D 391 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7133 (tm-30) REVERT: E 199 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6155 (t80) REVERT: E 265 ASN cc_start: 0.9136 (OUTLIER) cc_final: 0.8731 (t0) REVERT: E 285 ARG cc_start: 0.9170 (ptp-110) cc_final: 0.8914 (ttm110) REVERT: E 289 LEU cc_start: 0.9498 (mm) cc_final: 0.9275 (mp) REVERT: E 316 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7337 (pmm) REVERT: E 327 LYS cc_start: 0.8844 (tppt) cc_final: 0.8520 (tppt) REVERT: l 1 MET cc_start: 0.4293 (ppp) cc_final: 0.2387 (tmt) REVERT: F 199 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.6034 (t80) REVERT: F 223 TYR cc_start: 0.8755 (t80) cc_final: 0.8362 (t80) REVERT: F 265 ASN cc_start: 0.9088 (OUTLIER) cc_final: 0.8683 (t0) REVERT: F 391 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: M 59 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8771 (mm-30) REVERT: M 178 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8483 (mm-30) REVERT: G 219 PHE cc_start: 0.8956 (m-80) cc_final: 0.8607 (m-80) REVERT: G 265 ASN cc_start: 0.9181 (t0) cc_final: 0.8751 (t0) REVERT: G 285 ARG cc_start: 0.8777 (mmm-85) cc_final: 0.8162 (mmm-85) REVERT: N 314 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.5864 (pp) REVERT: N 389 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8172 (tm) REVERT: n 8 TYR cc_start: 0.4075 (p90) cc_final: 0.3772 (p90) REVERT: n 51 LEU cc_start: 0.1447 (OUTLIER) cc_final: 0.0947 (tp) outliers start: 224 outliers final: 93 residues processed: 664 average time/residue: 1.2559 time to fit residues: 1137.8376 Evaluate side-chains 588 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 472 time to evaluate : 5.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 305 LEU Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 16 MET Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain J residue 345 ARG Chi-restraints excluded: chain c residue 9 ASP Chi-restraints excluded: chain c residue 29 ILE Chi-restraints excluded: chain c residue 52 SER Chi-restraints excluded: chain j residue 12 VAL Chi-restraints excluded: chain j residue 51 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain l residue 77 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 301 ILE Chi-restraints excluded: chain M residue 305 LEU Chi-restraints excluded: chain f residue 16 MET Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 676 optimal weight: 0.5980 chunk 460 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 604 optimal weight: 3.9990 chunk 335 optimal weight: 5.9990 chunk 692 optimal weight: 4.9990 chunk 561 optimal weight: 0.0570 chunk 0 optimal weight: 5.9990 chunk 414 optimal weight: 2.9990 chunk 728 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 55 GLN ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 65457 Z= 0.172 Angle : 0.554 10.733 88396 Z= 0.278 Chirality : 0.044 0.238 10598 Planarity : 0.003 0.052 11312 Dihedral : 8.165 56.515 9517 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.91 % Allowed : 18.92 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.09), residues: 8470 helix: 2.05 (0.08), residues: 4081 sheet: 0.55 (0.16), residues: 1057 loop : -0.17 (0.11), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 44 HIS 0.002 0.000 HIS A 266 PHE 0.010 0.001 PHE k 69 TYR 0.017 0.001 TYR l 8 ARG 0.010 0.000 ARG F 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 491 time to evaluate : 5.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.5938 (t80) REVERT: A 252 GLU cc_start: 0.8423 (tt0) cc_final: 0.8065 (tt0) REVERT: A 268 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8725 (tppt) REVERT: A 316 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.6950 (pmm) REVERT: A 327 LYS cc_start: 0.8891 (tppt) cc_final: 0.8551 (tppt) REVERT: A 391 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: H 301 ILE cc_start: 0.1215 (OUTLIER) cc_final: 0.0872 (mt) REVERT: H 316 MET cc_start: -0.1027 (tpt) cc_final: -0.1294 (tpp) REVERT: a 5 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7591 (ttp80) REVERT: a 38 GLN cc_start: 0.7881 (mt0) cc_final: 0.7386 (mm-40) REVERT: h 51 LEU cc_start: 0.0908 (OUTLIER) cc_final: 0.0410 (tp) REVERT: B 44 TRP cc_start: 0.7970 (m100) cc_final: 0.7725 (m100) REVERT: B 193 MET cc_start: 0.8585 (tpt) cc_final: 0.7998 (tpt) REVERT: I 178 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8388 (mm-30) REVERT: b 38 GLN cc_start: 0.7404 (mt0) cc_final: 0.7163 (mt0) REVERT: b 47 ASP cc_start: 0.8682 (p0) cc_final: 0.8472 (p0) REVERT: i 1 MET cc_start: 0.3598 (ppp) cc_final: 0.3240 (ppp) REVERT: C 199 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.6020 (t80) REVERT: C 265 ASN cc_start: 0.9110 (OUTLIER) cc_final: 0.8793 (t0) REVERT: C 277 LYS cc_start: 0.7830 (mppt) cc_final: 0.7554 (mppt) REVERT: C 445 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8987 (tttm) REVERT: J 345 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8175 (tmt-80) REVERT: c 5 ARG cc_start: 0.8277 (ttp80) cc_final: 0.8023 (ttp80) REVERT: j 51 LEU cc_start: 0.1232 (OUTLIER) cc_final: 0.0884 (tp) REVERT: D 193 MET cc_start: 0.8433 (tpt) cc_final: 0.8068 (tpt) REVERT: D 199 TYR cc_start: 0.6724 (OUTLIER) cc_final: 0.5777 (t80) REVERT: K 314 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.5670 (pp) REVERT: E 199 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6133 (t80) REVERT: E 265 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8704 (t0) REVERT: E 285 ARG cc_start: 0.9190 (ptp-110) cc_final: 0.8957 (ttm110) REVERT: E 327 LYS cc_start: 0.8816 (tppt) cc_final: 0.8466 (tppt) REVERT: l 7 LEU cc_start: 0.2210 (pp) cc_final: 0.1853 (tp) REVERT: l 8 TYR cc_start: 0.4063 (m-80) cc_final: 0.3790 (m-10) REVERT: l 51 LEU cc_start: 0.1825 (OUTLIER) cc_final: 0.1450 (tp) REVERT: F 223 TYR cc_start: 0.8757 (t80) cc_final: 0.8333 (t80) REVERT: F 265 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8670 (t0) REVERT: M 178 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8503 (mm-30) REVERT: M 211 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6231 (tmt) REVERT: G 219 PHE cc_start: 0.8986 (m-80) cc_final: 0.8630 (m-80) REVERT: G 265 ASN cc_start: 0.9160 (OUTLIER) cc_final: 0.8722 (t0) REVERT: G 285 ARG cc_start: 0.8794 (mmm-85) cc_final: 0.8226 (mmm-85) REVERT: G 316 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7397 (pmm) REVERT: N 314 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5763 (pp) REVERT: N 389 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8162 (tm) REVERT: n 8 TYR cc_start: 0.4159 (p90) cc_final: 0.3866 (p90) REVERT: n 51 LEU cc_start: 0.1337 (OUTLIER) cc_final: -0.0009 (mm) outliers start: 199 outliers final: 109 residues processed: 647 average time/residue: 1.2015 time to fit residues: 1056.9632 Evaluate side-chains 599 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 467 time to evaluate : 5.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 305 LEU Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 16 MET Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 345 ARG Chi-restraints excluded: chain c residue 9 ASP Chi-restraints excluded: chain c residue 16 MET Chi-restraints excluded: chain c residue 29 ILE Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain j residue 12 VAL Chi-restraints excluded: chain j residue 51 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain k residue 68 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 342 ILE Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain l residue 77 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 211 MET Chi-restraints excluded: chain M residue 305 LEU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain N residue 276 VAL Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 273 optimal weight: 30.0000 chunk 731 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 476 optimal weight: 30.0000 chunk 200 optimal weight: 6.9990 chunk 812 optimal weight: 9.9990 chunk 674 optimal weight: 20.0000 chunk 376 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 268 optimal weight: 4.9990 chunk 426 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 ASN g 70 ASN n 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 65457 Z= 0.318 Angle : 0.595 12.264 88396 Z= 0.299 Chirality : 0.045 0.294 10598 Planarity : 0.003 0.041 11312 Dihedral : 7.983 59.551 9515 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.19 % Allowed : 19.23 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.09), residues: 8470 helix: 1.99 (0.08), residues: 4067 sheet: 0.65 (0.16), residues: 1092 loop : -0.31 (0.10), residues: 3311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 44 HIS 0.002 0.000 HIS K 401 PHE 0.010 0.001 PHE A 195 TYR 0.014 0.001 TYR C 223 ARG 0.008 0.000 ARG J 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 485 time to evaluate : 5.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 TYR cc_start: 0.7044 (OUTLIER) cc_final: 0.5938 (t80) REVERT: A 252 GLU cc_start: 0.8426 (tt0) cc_final: 0.8098 (tt0) REVERT: A 265 ASN cc_start: 0.9139 (t0) cc_final: 0.8917 (t0) REVERT: A 268 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8662 (tppt) REVERT: A 316 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7097 (pmm) REVERT: A 327 LYS cc_start: 0.8933 (tppt) cc_final: 0.8590 (tppt) REVERT: A 391 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: H 301 ILE cc_start: 0.1263 (OUTLIER) cc_final: 0.0917 (mt) REVERT: a 5 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7702 (ttp80) REVERT: a 38 GLN cc_start: 0.7876 (mt0) cc_final: 0.7388 (mm-40) REVERT: a 47 ASP cc_start: 0.8558 (p0) cc_final: 0.8300 (p0) REVERT: h 42 VAL cc_start: -0.0144 (OUTLIER) cc_final: -0.0352 (t) REVERT: h 51 LEU cc_start: 0.0982 (OUTLIER) cc_final: 0.0495 (tp) REVERT: B 193 MET cc_start: 0.8670 (tpt) cc_final: 0.8084 (tpt) REVERT: b 47 ASP cc_start: 0.8716 (p0) cc_final: 0.8490 (p0) REVERT: b 88 SER cc_start: 0.9080 (m) cc_final: 0.8654 (t) REVERT: i 8 TYR cc_start: 0.4338 (p90) cc_final: 0.3978 (p90) REVERT: i 51 LEU cc_start: 0.0790 (OUTLIER) cc_final: 0.0211 (tp) REVERT: C 265 ASN cc_start: 0.9120 (OUTLIER) cc_final: 0.8804 (t0) REVERT: C 277 LYS cc_start: 0.7924 (mppt) cc_final: 0.7640 (mppt) REVERT: C 316 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7386 (pmm) REVERT: J 250 ILE cc_start: 0.6585 (OUTLIER) cc_final: 0.6327 (pt) REVERT: c 5 ARG cc_start: 0.8280 (ttp80) cc_final: 0.8069 (ttt-90) REVERT: j 51 LEU cc_start: 0.1587 (OUTLIER) cc_final: 0.1246 (tp) REVERT: D 193 MET cc_start: 0.8488 (tpt) cc_final: 0.8116 (tpt) REVERT: D 199 TYR cc_start: 0.6733 (OUTLIER) cc_final: 0.5793 (t80) REVERT: D 391 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: K 314 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5702 (pp) REVERT: E 199 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.6118 (t80) REVERT: E 265 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8682 (t0) REVERT: E 285 ARG cc_start: 0.9196 (ptp-110) cc_final: 0.8952 (ttm110) REVERT: E 316 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7356 (pmm) REVERT: E 327 LYS cc_start: 0.8881 (tppt) cc_final: 0.8531 (tppt) REVERT: L 211 MET cc_start: 0.5802 (tpt) cc_final: 0.4923 (tmt) REVERT: l 1 MET cc_start: 0.4197 (ppp) cc_final: 0.2451 (tmt) REVERT: l 7 LEU cc_start: 0.2457 (pp) cc_final: 0.1999 (tp) REVERT: l 51 LEU cc_start: 0.1824 (OUTLIER) cc_final: 0.1459 (tp) REVERT: F 43 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8252 (mmtt) REVERT: F 199 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.5804 (t80) REVERT: F 223 TYR cc_start: 0.8766 (t80) cc_final: 0.8330 (t80) REVERT: F 265 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8660 (t0) REVERT: F 316 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6920 (pmm) REVERT: F 327 LYS cc_start: 0.8857 (tppt) cc_final: 0.8480 (tppt) REVERT: F 391 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7088 (tm-30) REVERT: M 178 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8547 (mm-30) REVERT: M 211 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.6223 (tmt) REVERT: m 1 MET cc_start: 0.4240 (ppp) cc_final: 0.2972 (pp-130) REVERT: G 219 PHE cc_start: 0.8998 (m-80) cc_final: 0.8665 (m-80) REVERT: G 265 ASN cc_start: 0.9188 (OUTLIER) cc_final: 0.8752 (t0) REVERT: G 285 ARG cc_start: 0.8840 (mmm-85) cc_final: 0.8244 (mmm-85) REVERT: G 288 TYR cc_start: 0.9112 (m-80) cc_final: 0.8582 (m-10) REVERT: G 316 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7367 (pmm) REVERT: G 386 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: N 314 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5666 (pp) REVERT: N 389 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8133 (tm) REVERT: n 51 LEU cc_start: 0.1470 (OUTLIER) cc_final: 0.0148 (mm) outliers start: 218 outliers final: 114 residues processed: 656 average time/residue: 1.1484 time to fit residues: 1035.2814 Evaluate side-chains 611 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 466 time to evaluate : 5.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 305 LEU Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 16 MET Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 88 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain c residue 9 ASP Chi-restraints excluded: chain c residue 16 MET Chi-restraints excluded: chain c residue 29 ILE Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 95 VAL Chi-restraints excluded: chain j residue 51 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 27 ILE Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain d residue 52 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain l residue 77 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 211 MET Chi-restraints excluded: chain M residue 305 LEU Chi-restraints excluded: chain m residue 15 ARG Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 783 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 463 optimal weight: 2.9990 chunk 593 optimal weight: 30.0000 chunk 459 optimal weight: 0.0670 chunk 684 optimal weight: 4.9990 chunk 453 optimal weight: 5.9990 chunk 809 optimal weight: 1.9990 chunk 506 optimal weight: 7.9990 chunk 493 optimal weight: 4.9990 chunk 373 optimal weight: 4.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 65457 Z= 0.294 Angle : 0.598 11.840 88396 Z= 0.300 Chirality : 0.045 0.269 10598 Planarity : 0.003 0.051 11312 Dihedral : 7.577 58.903 9515 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.78 % Allowed : 19.80 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.09), residues: 8470 helix: 1.94 (0.08), residues: 4074 sheet: 0.60 (0.16), residues: 1057 loop : -0.33 (0.10), residues: 3339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 44 HIS 0.001 0.000 HIS K 401 PHE 0.014 0.001 PHE N 195 TYR 0.023 0.001 TYR N 288 ARG 0.008 0.000 ARG N 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 487 time to evaluate : 5.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.5960 (t80) REVERT: A 265 ASN cc_start: 0.9130 (t0) cc_final: 0.8865 (t0) REVERT: A 268 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8674 (tppt) REVERT: A 316 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7086 (pmm) REVERT: A 327 LYS cc_start: 0.8947 (tppt) cc_final: 0.8609 (tppt) REVERT: A 391 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7185 (tm-30) REVERT: a 38 GLN cc_start: 0.7871 (mt0) cc_final: 0.7344 (mm-40) REVERT: h 42 VAL cc_start: -0.0092 (OUTLIER) cc_final: -0.0300 (t) REVERT: h 51 LEU cc_start: 0.0973 (OUTLIER) cc_final: 0.0488 (tp) REVERT: B 193 MET cc_start: 0.8681 (tpt) cc_final: 0.8209 (tpt) REVERT: b 16 MET cc_start: 0.7834 (tpp) cc_final: 0.7560 (ttm) REVERT: b 38 GLN cc_start: 0.7547 (mt0) cc_final: 0.7319 (mm-40) REVERT: b 47 ASP cc_start: 0.8708 (p0) cc_final: 0.8466 (p0) REVERT: b 88 SER cc_start: 0.9091 (m) cc_final: 0.8637 (t) REVERT: i 7 LEU cc_start: 0.2827 (mp) cc_final: 0.1941 (tp) REVERT: i 51 LEU cc_start: 0.0705 (OUTLIER) cc_final: 0.0104 (tp) REVERT: C 265 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8753 (t0) REVERT: C 277 LYS cc_start: 0.7951 (mppt) cc_final: 0.7668 (mppt) REVERT: C 316 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7412 (pmm) REVERT: C 445 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8966 (tttm) REVERT: J 250 ILE cc_start: 0.6530 (OUTLIER) cc_final: 0.6239 (pt) REVERT: c 5 ARG cc_start: 0.8286 (ttp80) cc_final: 0.8055 (ttt-90) REVERT: j 8 TYR cc_start: 0.3978 (p90) cc_final: 0.3479 (p90) REVERT: j 51 LEU cc_start: 0.1534 (OUTLIER) cc_final: 0.1184 (tp) REVERT: D 43 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8729 (tppt) REVERT: D 193 MET cc_start: 0.8516 (tpt) cc_final: 0.8163 (tpt) REVERT: D 199 TYR cc_start: 0.6726 (OUTLIER) cc_final: 0.5755 (t80) REVERT: D 391 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: K 314 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5668 (pp) REVERT: E 199 TYR cc_start: 0.7095 (OUTLIER) cc_final: 0.6099 (t80) REVERT: E 265 ASN cc_start: 0.9125 (OUTLIER) cc_final: 0.8685 (t0) REVERT: E 285 ARG cc_start: 0.9202 (ptp-110) cc_final: 0.8938 (ttm110) REVERT: E 316 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7350 (pmm) REVERT: E 327 LYS cc_start: 0.8907 (tppt) cc_final: 0.8574 (tppt) REVERT: L 211 MET cc_start: 0.5749 (tpt) cc_final: 0.4782 (tmt) REVERT: l 1 MET cc_start: 0.4237 (ppp) cc_final: 0.2515 (tmt) REVERT: l 7 LEU cc_start: 0.2415 (pp) cc_final: 0.1946 (tp) REVERT: l 51 LEU cc_start: 0.1930 (OUTLIER) cc_final: 0.1546 (tp) REVERT: F 43 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8239 (mmtt) REVERT: F 199 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.5778 (t80) REVERT: F 223 TYR cc_start: 0.8779 (t80) cc_final: 0.8328 (t80) REVERT: F 265 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8667 (t0) REVERT: F 327 LYS cc_start: 0.8891 (tppt) cc_final: 0.8502 (tppt) REVERT: F 391 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: M 178 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8560 (mm-30) REVERT: M 316 MET cc_start: 0.1197 (OUTLIER) cc_final: 0.0837 (ttt) REVERT: G 199 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6265 (t80) REVERT: G 219 PHE cc_start: 0.9002 (m-80) cc_final: 0.8626 (m-80) REVERT: G 265 ASN cc_start: 0.9180 (OUTLIER) cc_final: 0.8738 (t0) REVERT: G 288 TYR cc_start: 0.9111 (m-80) cc_final: 0.8608 (m-10) REVERT: G 316 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7375 (pmm) REVERT: G 386 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8525 (tt0) REVERT: N 389 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8125 (tm) REVERT: n 51 LEU cc_start: 0.1334 (OUTLIER) cc_final: 0.0077 (mm) outliers start: 190 outliers final: 114 residues processed: 629 average time/residue: 1.2018 time to fit residues: 1037.7732 Evaluate side-chains 613 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 469 time to evaluate : 5.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 16 MET Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain c residue 9 ASP Chi-restraints excluded: chain c residue 16 MET Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 95 VAL Chi-restraints excluded: chain j residue 51 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 27 ILE Chi-restraints excluded: chain d residue 52 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain l residue 77 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 305 LEU Chi-restraints excluded: chain M residue 316 MET Chi-restraints excluded: chain m residue 15 ARG Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain N residue 494 GLU Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 52 SER Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 500 optimal weight: 8.9990 chunk 323 optimal weight: 3.9990 chunk 483 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 514 optimal weight: 7.9990 chunk 551 optimal weight: 1.9990 chunk 400 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 636 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 55 GLN ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN g 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 65457 Z= 0.229 Angle : 0.587 11.440 88396 Z= 0.295 Chirality : 0.044 0.242 10598 Planarity : 0.003 0.040 11312 Dihedral : 6.948 59.443 9515 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.60 % Allowed : 20.24 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.09), residues: 8470 helix: 2.00 (0.08), residues: 4074 sheet: 0.55 (0.16), residues: 1050 loop : -0.34 (0.10), residues: 3346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 44 HIS 0.001 0.000 HIS K 401 PHE 0.015 0.001 PHE C 281 TYR 0.022 0.001 TYR N 288 ARG 0.009 0.000 ARG a 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 478 time to evaluate : 5.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.5978 (t80) REVERT: A 265 ASN cc_start: 0.9134 (t0) cc_final: 0.8870 (t0) REVERT: A 268 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8677 (tppt) REVERT: A 316 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7071 (pmm) REVERT: A 327 LYS cc_start: 0.8943 (tppt) cc_final: 0.8582 (tppt) REVERT: A 391 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: a 38 GLN cc_start: 0.7853 (mt0) cc_final: 0.7329 (mm-40) REVERT: a 56 ILE cc_start: 0.8787 (mt) cc_final: 0.8570 (tp) REVERT: h 42 VAL cc_start: 0.0061 (OUTLIER) cc_final: -0.0161 (t) REVERT: h 51 LEU cc_start: 0.0938 (OUTLIER) cc_final: 0.0430 (tp) REVERT: B 193 MET cc_start: 0.8683 (tpt) cc_final: 0.8261 (tpt) REVERT: b 47 ASP cc_start: 0.8717 (p0) cc_final: 0.8450 (p0) REVERT: b 88 SER cc_start: 0.9088 (m) cc_final: 0.8654 (t) REVERT: i 7 LEU cc_start: 0.2620 (mp) cc_final: 0.1826 (tp) REVERT: i 51 LEU cc_start: 0.0627 (OUTLIER) cc_final: 0.0050 (tp) REVERT: C 265 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8740 (t0) REVERT: C 277 LYS cc_start: 0.7911 (mppt) cc_final: 0.7641 (mppt) REVERT: C 316 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7395 (pmm) REVERT: C 445 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8969 (tttm) REVERT: J 250 ILE cc_start: 0.6451 (OUTLIER) cc_final: 0.6178 (pt) REVERT: J 363 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7383 (pm20) REVERT: j 8 TYR cc_start: 0.3916 (p90) cc_final: 0.3410 (p90) REVERT: D 193 MET cc_start: 0.8537 (tpt) cc_final: 0.8142 (tpt) REVERT: D 199 TYR cc_start: 0.6761 (OUTLIER) cc_final: 0.6025 (t80) REVERT: D 391 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: K 314 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5643 (pp) REVERT: E 199 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6070 (t80) REVERT: E 265 ASN cc_start: 0.9106 (OUTLIER) cc_final: 0.8656 (t0) REVERT: E 285 ARG cc_start: 0.9216 (ptp-110) cc_final: 0.8948 (ttm110) REVERT: E 316 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7296 (pmm) REVERT: E 327 LYS cc_start: 0.8927 (tppt) cc_final: 0.8613 (tppt) REVERT: L 211 MET cc_start: 0.5794 (tpt) cc_final: 0.4858 (tmt) REVERT: l 69 PHE cc_start: 0.3878 (OUTLIER) cc_final: 0.3289 (p90) REVERT: F 43 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8211 (mmtt) REVERT: F 199 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.5631 (t80) REVERT: F 223 TYR cc_start: 0.8777 (t80) cc_final: 0.8300 (t80) REVERT: F 265 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8667 (t0) REVERT: F 316 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.6964 (pmm) REVERT: F 327 LYS cc_start: 0.8884 (tppt) cc_final: 0.8487 (tppt) REVERT: F 391 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: M 178 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8559 (mm-30) REVERT: M 316 MET cc_start: 0.1133 (OUTLIER) cc_final: 0.0774 (ttt) REVERT: G 199 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6245 (t80) REVERT: G 219 PHE cc_start: 0.9010 (m-80) cc_final: 0.8633 (m-80) REVERT: G 265 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8718 (t0) REVERT: G 285 ARG cc_start: 0.9084 (mmm-85) cc_final: 0.8406 (mmm-85) REVERT: G 288 TYR cc_start: 0.9117 (m-80) cc_final: 0.8613 (m-10) REVERT: G 316 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7387 (pmm) REVERT: G 386 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: N 314 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5495 (pp) REVERT: N 389 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8079 (tm) REVERT: n 51 LEU cc_start: 0.1259 (OUTLIER) cc_final: 0.0016 (mm) outliers start: 178 outliers final: 112 residues processed: 614 average time/residue: 1.1473 time to fit residues: 966.4692 Evaluate side-chains 613 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 469 time to evaluate : 5.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 16 MET Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 363 GLU Chi-restraints excluded: chain c residue 9 ASP Chi-restraints excluded: chain c residue 16 MET Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 95 VAL Chi-restraints excluded: chain j residue 39 ILE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 16 MET Chi-restraints excluded: chain d residue 27 ILE Chi-restraints excluded: chain d residue 52 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain l residue 69 PHE Chi-restraints excluded: chain l residue 77 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 316 MET Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain m residue 15 ARG Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain N residue 494 GLU Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 52 SER Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 736 optimal weight: 3.9990 chunk 775 optimal weight: 4.9990 chunk 707 optimal weight: 20.0000 chunk 754 optimal weight: 0.7980 chunk 454 optimal weight: 0.9990 chunk 328 optimal weight: 8.9990 chunk 592 optimal weight: 8.9990 chunk 231 optimal weight: 9.9990 chunk 681 optimal weight: 10.0000 chunk 713 optimal weight: 20.0000 chunk 751 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 38 GLN ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 55 GLN L 229 ASN g 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 65457 Z= 0.425 Angle : 0.650 10.846 88396 Z= 0.327 Chirality : 0.047 0.215 10598 Planarity : 0.004 0.043 11312 Dihedral : 6.904 59.906 9515 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.62 % Allowed : 20.32 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.09), residues: 8470 helix: 1.85 (0.08), residues: 4053 sheet: 0.51 (0.16), residues: 1050 loop : -0.38 (0.10), residues: 3367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 44 HIS 0.002 0.001 HIS K 401 PHE 0.013 0.002 PHE j 69 TYR 0.029 0.001 TYR N 288 ARG 0.008 0.001 ARG c 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 482 time to evaluate : 6.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6007 (t80) REVERT: A 265 ASN cc_start: 0.9132 (t0) cc_final: 0.8857 (t0) REVERT: A 268 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8686 (tppt) REVERT: A 272 ARG cc_start: 0.8705 (mtm180) cc_final: 0.8362 (mtm180) REVERT: A 316 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7268 (pmm) REVERT: A 327 LYS cc_start: 0.8974 (tppt) cc_final: 0.8634 (tppt) REVERT: A 391 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7287 (tm-30) REVERT: a 38 GLN cc_start: 0.7909 (mt0) cc_final: 0.7388 (mm-40) REVERT: a 56 ILE cc_start: 0.8806 (mt) cc_final: 0.8502 (tp) REVERT: h 42 VAL cc_start: 0.0202 (OUTLIER) cc_final: -0.0004 (t) REVERT: h 51 LEU cc_start: 0.0997 (OUTLIER) cc_final: 0.0528 (tp) REVERT: B 193 MET cc_start: 0.8781 (tpt) cc_final: 0.8362 (tpt) REVERT: b 47 ASP cc_start: 0.8724 (p0) cc_final: 0.8483 (p0) REVERT: b 88 SER cc_start: 0.9126 (m) cc_final: 0.8701 (t) REVERT: i 51 LEU cc_start: 0.0828 (OUTLIER) cc_final: 0.0235 (tp) REVERT: C 265 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8726 (t0) REVERT: C 277 LYS cc_start: 0.8016 (mppt) cc_final: 0.7713 (mppt) REVERT: C 285 ARG cc_start: 0.8736 (mmm-85) cc_final: 0.8456 (mmm-85) REVERT: C 316 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7493 (pmm) REVERT: C 445 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8965 (tttm) REVERT: J 520 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8956 (p) REVERT: j 8 TYR cc_start: 0.3926 (p90) cc_final: 0.3408 (p90) REVERT: D 193 MET cc_start: 0.8627 (tpt) cc_final: 0.8199 (tpt) REVERT: D 199 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.5726 (t80) REVERT: D 391 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: E 199 TYR cc_start: 0.7148 (OUTLIER) cc_final: 0.6166 (t80) REVERT: E 265 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8713 (t0) REVERT: E 285 ARG cc_start: 0.9197 (ptp-110) cc_final: 0.8900 (ttm110) REVERT: E 316 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7437 (pmm) REVERT: E 327 LYS cc_start: 0.8946 (tppt) cc_final: 0.8618 (tppt) REVERT: L 211 MET cc_start: 0.5625 (tpt) cc_final: 0.4539 (tmt) REVERT: l 1 MET cc_start: 0.4228 (ppp) cc_final: 0.1133 (tmt) REVERT: l 51 LEU cc_start: 0.1079 (OUTLIER) cc_final: -0.0453 (mt) REVERT: F 43 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8262 (mmtt) REVERT: F 199 TYR cc_start: 0.6920 (OUTLIER) cc_final: 0.5785 (t80) REVERT: F 219 PHE cc_start: 0.8820 (m-80) cc_final: 0.8390 (m-80) REVERT: F 223 TYR cc_start: 0.8761 (t80) cc_final: 0.8308 (t80) REVERT: F 265 ASN cc_start: 0.9096 (OUTLIER) cc_final: 0.8683 (t0) REVERT: F 316 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7108 (pmm) REVERT: F 319 ARG cc_start: 0.8567 (mmm-85) cc_final: 0.8129 (mmm160) REVERT: F 327 LYS cc_start: 0.8938 (tppt) cc_final: 0.8543 (tppt) REVERT: F 391 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7138 (tm-30) REVERT: M 178 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8577 (mm-30) REVERT: M 316 MET cc_start: 0.1100 (OUTLIER) cc_final: 0.0748 (ttt) REVERT: G 199 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6352 (t80) REVERT: G 219 PHE cc_start: 0.9015 (m-80) cc_final: 0.8662 (m-80) REVERT: G 265 ASN cc_start: 0.9193 (OUTLIER) cc_final: 0.8740 (t0) REVERT: G 285 ARG cc_start: 0.9085 (mmm-85) cc_final: 0.8409 (mmm-85) REVERT: G 288 TYR cc_start: 0.9129 (m-80) cc_final: 0.8635 (m-10) REVERT: G 316 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7387 (pmm) REVERT: N 314 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5309 (pp) REVERT: N 389 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8073 (tm) REVERT: g 28 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8594 (mt) REVERT: n 51 LEU cc_start: 0.1353 (OUTLIER) cc_final: 0.0110 (mm) outliers start: 179 outliers final: 115 residues processed: 620 average time/residue: 1.2347 time to fit residues: 1038.9700 Evaluate side-chains 619 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 474 time to evaluate : 5.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain a residue 16 MET Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain J residue 520 THR Chi-restraints excluded: chain c residue 9 ASP Chi-restraints excluded: chain c residue 29 ILE Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 95 VAL Chi-restraints excluded: chain j residue 53 ASN Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 230 VAL Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 16 MET Chi-restraints excluded: chain d residue 95 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain l residue 77 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 316 MET Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain m residue 15 ARG Chi-restraints excluded: chain m residue 72 TYR Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 495 optimal weight: 2.9990 chunk 797 optimal weight: 10.0000 chunk 486 optimal weight: 0.8980 chunk 378 optimal weight: 3.9990 chunk 554 optimal weight: 30.0000 chunk 836 optimal weight: 30.0000 chunk 770 optimal weight: 1.9990 chunk 666 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 514 optimal weight: 20.0000 chunk 408 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 65457 Z= 0.225 Angle : 0.610 11.701 88396 Z= 0.305 Chirality : 0.045 0.213 10598 Planarity : 0.003 0.042 11312 Dihedral : 6.520 59.341 9514 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.03 % Allowed : 20.91 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.09), residues: 8470 helix: 1.94 (0.08), residues: 4081 sheet: 0.52 (0.16), residues: 1050 loop : -0.38 (0.10), residues: 3339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 44 HIS 0.001 0.000 HIS M 266 PHE 0.012 0.001 PHE n 69 TYR 0.024 0.001 TYR N 288 ARG 0.011 0.000 ARG A 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 477 time to evaluate : 6.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.6036 (t80) REVERT: A 265 ASN cc_start: 0.9127 (t0) cc_final: 0.8853 (t0) REVERT: A 268 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8692 (tppt) REVERT: A 327 LYS cc_start: 0.8952 (tppt) cc_final: 0.8585 (tppt) REVERT: A 391 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: a 38 GLN cc_start: 0.7844 (mt0) cc_final: 0.7327 (mm-40) REVERT: a 56 ILE cc_start: 0.8760 (mt) cc_final: 0.8558 (tp) REVERT: h 51 LEU cc_start: 0.0791 (OUTLIER) cc_final: 0.0309 (tp) REVERT: B 193 MET cc_start: 0.8787 (tpt) cc_final: 0.8365 (tpt) REVERT: b 47 ASP cc_start: 0.8718 (p0) cc_final: 0.8457 (p0) REVERT: b 88 SER cc_start: 0.9115 (m) cc_final: 0.8680 (t) REVERT: C 265 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8756 (t0) REVERT: C 277 LYS cc_start: 0.7962 (mppt) cc_final: 0.7652 (mppt) REVERT: C 445 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8960 (tttm) REVERT: j 8 TYR cc_start: 0.3987 (p90) cc_final: 0.3459 (p90) REVERT: D 193 MET cc_start: 0.8599 (tpt) cc_final: 0.8181 (tpt) REVERT: D 391 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: E 199 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.6236 (t80) REVERT: E 265 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8710 (t0) REVERT: E 277 LYS cc_start: 0.7956 (mppt) cc_final: 0.7728 (mppt) REVERT: E 285 ARG cc_start: 0.9245 (ptp-110) cc_final: 0.8963 (ttm110) REVERT: E 316 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7331 (pmm) REVERT: E 327 LYS cc_start: 0.8932 (tppt) cc_final: 0.8641 (tppt) REVERT: L 211 MET cc_start: 0.5631 (tpt) cc_final: 0.4584 (tmt) REVERT: l 1 MET cc_start: 0.4236 (ppp) cc_final: 0.1158 (tmt) REVERT: l 8 TYR cc_start: 0.4090 (m-80) cc_final: 0.3750 (m-10) REVERT: F 199 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.5677 (t80) REVERT: F 223 TYR cc_start: 0.8765 (t80) cc_final: 0.8326 (t80) REVERT: F 265 ASN cc_start: 0.9081 (OUTLIER) cc_final: 0.8687 (t0) REVERT: F 327 LYS cc_start: 0.8911 (tppt) cc_final: 0.8543 (tppt) REVERT: F 391 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: M 59 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8737 (mm-30) REVERT: M 178 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8523 (mm-30) REVERT: M 316 MET cc_start: 0.1217 (OUTLIER) cc_final: 0.0733 (ttt) REVERT: G 199 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.6324 (t80) REVERT: G 219 PHE cc_start: 0.9039 (m-80) cc_final: 0.8651 (m-80) REVERT: G 265 ASN cc_start: 0.9160 (OUTLIER) cc_final: 0.8700 (t0) REVERT: G 288 TYR cc_start: 0.9122 (m-80) cc_final: 0.8645 (m-10) REVERT: G 316 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7435 (pmm) REVERT: N 314 LEU cc_start: 0.5890 (OUTLIER) cc_final: 0.5296 (pp) REVERT: N 389 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8096 (tm) REVERT: n 51 LEU cc_start: 0.1344 (OUTLIER) cc_final: 0.0122 (mm) outliers start: 139 outliers final: 99 residues processed: 585 average time/residue: 1.2183 time to fit residues: 975.8359 Evaluate side-chains 588 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 468 time to evaluate : 5.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain a residue 16 MET Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 95 VAL Chi-restraints excluded: chain j residue 53 ASN Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 230 VAL Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain d residue 16 MET Chi-restraints excluded: chain d residue 27 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain l residue 77 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 316 MET Chi-restraints excluded: chain m residue 15 ARG Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 529 optimal weight: 0.9990 chunk 709 optimal weight: 0.0270 chunk 204 optimal weight: 0.8980 chunk 614 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 667 optimal weight: 6.9990 chunk 279 optimal weight: 0.8980 chunk 685 optimal weight: 7.9990 chunk 84 optimal weight: 30.0000 chunk 122 optimal weight: 0.8980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 290 GLN ** c 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 55 GLN g 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.135659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.072242 restraints weight = 124742.725| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.54 r_work: 0.2759 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 65457 Z= 0.163 Angle : 0.604 14.590 88396 Z= 0.299 Chirality : 0.044 0.276 10598 Planarity : 0.003 0.043 11312 Dihedral : 6.158 57.891 9514 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.67 % Favored : 97.32 % Rotamer: Outliers : 1.90 % Allowed : 21.08 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.09), residues: 8470 helix: 2.05 (0.08), residues: 4081 sheet: 0.54 (0.16), residues: 1050 loop : -0.37 (0.11), residues: 3339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 44 HIS 0.001 0.000 HIS J 401 PHE 0.012 0.001 PHE n 69 TYR 0.034 0.001 TYR N 288 ARG 0.011 0.000 ARG c 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20733.66 seconds wall clock time: 357 minutes 50.38 seconds (21470.38 seconds total)