Starting phenix.real_space_refine on Thu Sep 26 03:15:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz3_32903/09_2024/7wz3_32903.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz3_32903/09_2024/7wz3_32903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz3_32903/09_2024/7wz3_32903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz3_32903/09_2024/7wz3_32903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz3_32903/09_2024/7wz3_32903.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz3_32903/09_2024/7wz3_32903.cif" } resolution = 4.1 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= 0.019 sd= 0.164 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 364 5.16 5 C 36697 2.51 5 N 10202 2.21 5 O 11276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 265 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 58551 Number of models: 1 Model: "" Number of chains: 22 Chain: "a" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3949 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 12, 'TRANS': 507} Chain: "A" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3590 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 11, 'TRANS': 464} Chain breaks: 1 Chain: "b" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3580 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 9, 'TRANS': 467} Chain breaks: 1 Chain: "B" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2426 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 1 Chain: "D" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3259 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 421} Chain breaks: 4 Chain: "d" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3902 Classifications: {'peptide': 516} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 500} Chain: "E" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3936 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 17, 'TRANS': 494} Chain: "e" Number of atoms: 3921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3921 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 17, 'TRANS': 492} Chain: "g" Number of atoms: 3724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3724 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 16, 'TRANS': 464} Chain breaks: 1 Chain: "G" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3165 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 1 Chain: "h" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3927 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 14, 'TRANS': 496} Chain: "H" Number of atoms: 3898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3898 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 14, 'TRANS': 492} Chain: "Q" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3602 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 12, 'TRANS': 459} Chain breaks: 1 Chain: "q" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3688 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 12, 'TRANS': 470} Chain breaks: 1 Chain: "Z" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3907 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 13, 'TRANS': 495} Chain: "z" Number of atoms: 3915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3915 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 13, 'TRANS': 496} Chain: "g" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 27.35, per 1000 atoms: 0.47 Number of scatterers: 58551 At special positions: 0 Unit cell: (188.474, 196.382, 183.202, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 364 16.00 P 12 15.00 O 11276 8.00 N 10202 7.00 C 36697 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.33 Conformation dependent library (CDL) restraints added in 5.9 seconds 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14280 Finding SS restraints... Secondary structure from input PDB file: 310 helices and 91 sheets defined 56.6% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain 'a' and resid 14 through 32 removed outlier: 3.825A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 65 Processing helix chain 'a' and resid 69 through 86 removed outlier: 3.544A pdb=" N LYS a 73 " --> pdb=" O HIS a 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL a 74 " --> pdb=" O PRO a 70 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS a 76 " --> pdb=" O ALA a 72 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU a 77 " --> pdb=" O LYS a 73 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU a 81 " --> pdb=" O GLU a 77 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 110 removed outlier: 3.855A pdb=" N VAL a 93 " --> pdb=" O GLY a 89 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE a 95 " --> pdb=" O THR a 91 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU a 106 " --> pdb=" O LYS a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 134 removed outlier: 3.649A pdb=" N LEU a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 156 removed outlier: 4.009A pdb=" N SER a 155 " --> pdb=" O ALA a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 157 through 163 removed outlier: 5.736A pdb=" N ILE a 160 " --> pdb=" O SER a 157 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE a 161 " --> pdb=" O SER a 158 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE a 163 " --> pdb=" O ILE a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.319A pdb=" N MET a 171 " --> pdb=" O PHE a 167 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL a 172 " --> pdb=" O PHE a 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL a 173 " --> pdb=" O ALA a 169 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP a 174 " --> pdb=" O ASN a 170 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU a 177 " --> pdb=" O VAL a 173 " (cutoff:3.500A) Processing helix chain 'a' and resid 204 through 208 removed outlier: 3.622A pdb=" N GLU a 207 " --> pdb=" O SER a 204 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER a 208 " --> pdb=" O GLN a 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 204 through 208' Processing helix chain 'a' and resid 256 through 280 removed outlier: 3.565A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU a 273 " --> pdb=" O ASP a 269 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN a 276 " --> pdb=" O LYS a 272 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 304 removed outlier: 3.508A pdb=" N LYS a 298 " --> pdb=" O ASP a 294 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR a 299 " --> pdb=" O MET a 295 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE a 300 " --> pdb=" O CYS a 296 " (cutoff:3.500A) Processing helix chain 'a' and resid 312 through 324 removed outlier: 3.590A pdb=" N ARG a 318 " --> pdb=" O ARG a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 381 through 403 removed outlier: 3.632A pdb=" N GLU a 387 " --> pdb=" O PHE a 383 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG a 390 " --> pdb=" O ASP a 386 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER a 391 " --> pdb=" O GLU a 387 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS a 397 " --> pdb=" O HIS a 393 " (cutoff:3.500A) Processing helix chain 'a' and resid 413 through 431 removed outlier: 4.062A pdb=" N ILE a 421 " --> pdb=" O ALA a 417 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET a 430 " --> pdb=" O TYR a 426 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY a 431 " --> pdb=" O ALA a 427 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 445 removed outlier: 3.658A pdb=" N LEU a 445 " --> pdb=" O PHE a 441 " (cutoff:3.500A) Processing helix chain 'a' and resid 446 through 456 removed outlier: 3.951A pdb=" N VAL a 454 " --> pdb=" O ASN a 450 " (cutoff:3.500A) Processing helix chain 'a' and resid 459 through 477 removed outlier: 3.545A pdb=" N LEU a 463 " --> pdb=" O ASP a 459 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL a 464 " --> pdb=" O SER a 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA a 465 " --> pdb=" O THR a 461 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU a 473 " --> pdb=" O ALA a 469 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN a 475 " --> pdb=" O HIS a 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN a 477 " --> pdb=" O GLU a 473 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'A' and resid 15 through 32 removed outlier: 3.586A pdb=" N SER A 27 " --> pdb=" O MET A 23 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.827A pdb=" N ILE A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 86 removed outlier: 3.876A pdb=" N VAL A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.668A pdb=" N VAL A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 134 removed outlier: 3.676A pdb=" N VAL A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 156 removed outlier: 3.781A pdb=" N SER A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 164 through 178 removed outlier: 3.825A pdb=" N PHE A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.595A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 381 through 405 removed outlier: 3.901A pdb=" N MET A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.911A pdb=" N ILE A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 446 removed outlier: 3.684A pdb=" N ALA A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.709A pdb=" N VAL A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 477 removed outlier: 3.627A pdb=" N ALA A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 507 through 527 removed outlier: 3.613A pdb=" N LYS A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing helix chain 'b' and resid 22 through 40 removed outlier: 3.999A pdb=" N LEU b 26 " --> pdb=" O GLU b 22 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE b 35 " --> pdb=" O GLY b 31 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL b 39 " --> pdb=" O ILE b 35 " (cutoff:3.500A) Processing helix chain 'b' and resid 41 through 43 No H-bonds generated for 'chain 'b' and resid 41 through 43' Processing helix chain 'b' and resid 66 through 74 removed outlier: 3.526A pdb=" N ASN b 73 " --> pdb=" O THR b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 95 removed outlier: 3.602A pdb=" N VAL b 83 " --> pdb=" O PRO b 79 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU b 84 " --> pdb=" O ALA b 80 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL b 85 " --> pdb=" O ALA b 81 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL b 90 " --> pdb=" O ASP b 86 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN b 91 " --> pdb=" O MET b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 98 through 119 removed outlier: 3.569A pdb=" N THR b 103 " --> pdb=" O THR b 99 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU b 110 " --> pdb=" O ALA b 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER b 115 " --> pdb=" O ARG b 111 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA b 118 " --> pdb=" O GLU b 114 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 144 removed outlier: 3.583A pdb=" N GLY b 129 " --> pdb=" O THR b 125 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU b 132 " --> pdb=" O ALA b 128 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS b 135 " --> pdb=" O ARG b 131 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 167 removed outlier: 3.513A pdb=" N MET b 160 " --> pdb=" O ARG b 156 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN b 161 " --> pdb=" O GLN b 157 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.548A pdb=" N THR b 173 " --> pdb=" O LYS b 170 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 170 through 174' Processing helix chain 'b' and resid 175 through 191 removed outlier: 4.042A pdb=" N LYS b 181 " --> pdb=" O ASP b 177 " (cutoff:3.500A) Processing helix chain 'b' and resid 195 through 197 No H-bonds generated for 'chain 'b' and resid 195 through 197' Processing helix chain 'b' and resid 271 through 284 removed outlier: 3.699A pdb=" N LYS b 276 " --> pdb=" O LYS b 272 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE b 282 " --> pdb=" O LYS b 278 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS b 284 " --> pdb=" O GLU b 280 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 308 removed outlier: 3.731A pdb=" N LEU b 303 " --> pdb=" O TYR b 299 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE b 304 " --> pdb=" O PRO b 300 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY b 305 " --> pdb=" O GLU b 301 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA b 306 " --> pdb=" O GLN b 302 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA b 307 " --> pdb=" O LEU b 303 " (cutoff:3.500A) Processing helix chain 'b' and resid 316 through 327 removed outlier: 3.946A pdb=" N LEU b 323 " --> pdb=" O GLY b 319 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU b 325 " --> pdb=" O GLU b 321 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 403 removed outlier: 3.584A pdb=" N SER b 389 " --> pdb=" O GLU b 385 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL b 396 " --> pdb=" O ASP b 392 " (cutoff:3.500A) Processing helix chain 'b' and resid 411 through 425 removed outlier: 3.622A pdb=" N MET b 415 " --> pdb=" O GLY b 411 " (cutoff:3.500A) Processing helix chain 'b' and resid 429 through 454 removed outlier: 3.883A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA b 435 " --> pdb=" O LYS b 431 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU b 446 " --> pdb=" O ALA b 442 " (cutoff:3.500A) Proline residue: b 447 - end of helix Processing helix chain 'b' and resid 457 through 471 removed outlier: 3.652A pdb=" N VAL b 462 " --> pdb=" O SER b 458 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA b 463 " --> pdb=" O ALA b 459 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU b 465 " --> pdb=" O LEU b 461 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG b 466 " --> pdb=" O VAL b 462 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA b 467 " --> pdb=" O ALA b 463 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU b 471 " --> pdb=" O ALA b 467 " (cutoff:3.500A) Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 removed outlier: 3.801A pdb=" N ILE b 514 " --> pdb=" O ALA b 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 39 removed outlier: 3.727A pdb=" N LEU B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.597A pdb=" N LEU B 61 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 74 removed outlier: 3.526A pdb=" N LEU B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 95 removed outlier: 3.981A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN B 91 " --> pdb=" O MET B 87 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.658A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 145 removed outlier: 3.514A pdb=" N ALA B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 167 removed outlier: 3.557A pdb=" N MET B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.862A pdb=" N THR B 173 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 174' Processing helix chain 'B' and resid 175 through 191 removed outlier: 3.897A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 182 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 403 removed outlier: 3.618A pdb=" N VAL B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN B 399 " --> pdb=" O CYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 425 removed outlier: 3.506A pdb=" N MET B 415 " --> pdb=" O GLY B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 removed outlier: 3.700A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.779A pdb=" N ILE B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 471 removed outlier: 3.738A pdb=" N LEU B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B 466 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 517 removed outlier: 3.641A pdb=" N VAL B 513 " --> pdb=" O GLU B 509 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 514 " --> pdb=" O ALA B 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 49 removed outlier: 3.765A pdb=" N ARG D 34 " --> pdb=" O PRO D 30 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 73 through 80 removed outlier: 3.510A pdb=" N LYS D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 removed outlier: 3.823A pdb=" N LEU D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 100 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 125 removed outlier: 3.692A pdb=" N VAL D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 removed outlier: 3.513A pdb=" N LYS D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET D 151 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 172 removed outlier: 3.952A pdb=" N SER D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 189 removed outlier: 3.523A pdb=" N LEU D 183 " --> pdb=" O TYR D 179 " (cutoff:3.500A) Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.659A pdb=" N ASN D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET D 320 " --> pdb=" O PHE D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 341 removed outlier: 3.665A pdb=" N CYS D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 356 removed outlier: 3.539A pdb=" N MET D 355 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 356 " --> pdb=" O ALA D 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 352 through 356' Processing helix chain 'D' and resid 394 through 418 removed outlier: 3.583A pdb=" N VAL D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 442 removed outlier: 3.925A pdb=" N GLU D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG D 441 " --> pdb=" O THR D 437 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 459 removed outlier: 3.595A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET D 458 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 472 through 487 removed outlier: 4.050A pdb=" N VAL D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN D 482 " --> pdb=" O THR D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 531 removed outlier: 3.543A pdb=" N LEU D 519 " --> pdb=" O SER D 515 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 49 removed outlier: 3.502A pdb=" N ARG d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER d 36 " --> pdb=" O GLN d 32 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL d 44 " --> pdb=" O ALA d 40 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA d 45 " --> pdb=" O ALA d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 50 through 52 No H-bonds generated for 'chain 'd' and resid 50 through 52' Processing helix chain 'd' and resid 73 through 80 removed outlier: 3.636A pdb=" N ILE d 77 " --> pdb=" O ASP d 73 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU d 78 " --> pdb=" O GLY d 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN d 80 " --> pdb=" O THR d 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 73 through 80' Processing helix chain 'd' and resid 85 through 102 removed outlier: 3.585A pdb=" N MET d 90 " --> pdb=" O PRO d 86 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU d 91 " --> pdb=" O ALA d 87 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL d 92 " --> pdb=" O ALA d 88 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU d 93 " --> pdb=" O ARG d 89 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE d 100 " --> pdb=" O LYS d 96 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.658A pdb=" N VAL d 109 " --> pdb=" O GLY d 105 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE d 111 " --> pdb=" O THR d 107 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS d 126 " --> pdb=" O LYS d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 129 through 152 removed outlier: 3.644A pdb=" N GLU d 146 " --> pdb=" O GLU d 142 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET d 151 " --> pdb=" O ILE d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 159 through 173 removed outlier: 3.531A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER d 170 " --> pdb=" O SER d 166 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU d 171 " --> pdb=" O ALA d 167 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 195 Proline residue: d 185 - end of helix Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 268 through 292 removed outlier: 3.704A pdb=" N ARG d 280 " --> pdb=" O LEU d 276 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU d 286 " --> pdb=" O TYR d 282 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS d 292 " --> pdb=" O LYS d 288 " (cutoff:3.500A) Processing helix chain 'd' and resid 312 through 320 removed outlier: 3.859A pdb=" N ASN d 318 " --> pdb=" O LEU d 314 " (cutoff:3.500A) Processing helix chain 'd' and resid 329 through 341 removed outlier: 3.808A pdb=" N GLU d 334 " --> pdb=" O ARG d 330 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE d 335 " --> pdb=" O GLU d 331 " (cutoff:3.500A) Processing helix chain 'd' and resid 352 through 356 removed outlier: 3.838A pdb=" N MET d 355 " --> pdb=" O THR d 352 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU d 356 " --> pdb=" O ALA d 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 352 through 356' Processing helix chain 'd' and resid 394 through 418 removed outlier: 3.666A pdb=" N VAL d 411 " --> pdb=" O ASP d 407 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS d 417 " --> pdb=" O ARG d 413 " (cutoff:3.500A) Processing helix chain 'd' and resid 426 through 441 removed outlier: 3.674A pdb=" N ILE d 430 " --> pdb=" O GLY d 426 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU d 431 " --> pdb=" O ALA d 427 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU d 438 " --> pdb=" O LEU d 434 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG d 441 " --> pdb=" O THR d 437 " (cutoff:3.500A) Processing helix chain 'd' and resid 442 through 443 No H-bonds generated for 'chain 'd' and resid 442 through 443' Processing helix chain 'd' and resid 444 through 445 No H-bonds generated for 'chain 'd' and resid 444 through 445' Processing helix chain 'd' and resid 446 through 457 removed outlier: 4.007A pdb=" N CYS d 450 " --> pdb=" O MET d 446 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 469 Processing helix chain 'd' and resid 472 through 487 removed outlier: 3.727A pdb=" N THR d 476 " --> pdb=" O ASN d 472 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL d 477 " --> pdb=" O PRO d 473 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU d 479 " --> pdb=" O SER d 475 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN d 482 " --> pdb=" O THR d 478 " (cutoff:3.500A) Processing helix chain 'd' and resid 503 through 507 Processing helix chain 'd' and resid 512 through 531 removed outlier: 3.701A pdb=" N ALA d 522 " --> pdb=" O ALA d 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 46 removed outlier: 3.690A pdb=" N LEU E 32 " --> pdb=" O GLY E 28 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 79 removed outlier: 3.659A pdb=" N LEU E 76 " --> pdb=" O GLY E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 100 removed outlier: 3.985A pdb=" N MET E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 90 " --> pdb=" O ALA E 86 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU E 91 " --> pdb=" O LYS E 87 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER E 93 " --> pdb=" O MET E 89 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN E 96 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP E 97 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 124 removed outlier: 3.761A pdb=" N VAL E 107 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL E 109 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 149 removed outlier: 3.527A pdb=" N ILE E 131 " --> pdb=" O HIS E 127 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 171 removed outlier: 3.666A pdb=" N GLN E 165 " --> pdb=" O GLU E 161 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR E 169 " --> pdb=" O GLN E 165 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR E 170 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 179 through 195 removed outlier: 3.591A pdb=" N GLU E 185 " --> pdb=" O ARG E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 216 through 220 removed outlier: 3.573A pdb=" N THR E 220 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 293 removed outlier: 3.607A pdb=" N ALA E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN E 276 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE E 287 " --> pdb=" O PHE E 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 290 " --> pdb=" O MET E 286 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU E 292 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR E 293 " --> pdb=" O GLN E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 316 removed outlier: 3.781A pdb=" N GLN E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.512A pdb=" N GLU E 329 " --> pdb=" O GLY E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 413 removed outlier: 3.739A pdb=" N ARG E 398 " --> pdb=" O GLU E 394 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 436 removed outlier: 4.188A pdb=" N ILE E 425 " --> pdb=" O GLY E 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP E 436 " --> pdb=" O SER E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 454 removed outlier: 3.637A pdb=" N GLU E 454 " --> pdb=" O ALA E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 464 removed outlier: 3.528A pdb=" N LEU E 460 " --> pdb=" O ILE E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 479 removed outlier: 3.595A pdb=" N MET E 472 " --> pdb=" O PRO E 468 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 474 " --> pdb=" O GLN E 470 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL E 475 " --> pdb=" O THR E 471 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG E 476 " --> pdb=" O MET E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 503 removed outlier: 3.835A pdb=" N GLN E 502 " --> pdb=" O ASP E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 527 removed outlier: 3.782A pdb=" N ILE E 515 " --> pdb=" O LYS E 511 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR E 519 " --> pdb=" O ILE E 515 " (cutoff:3.500A) Processing helix chain 'e' and resid 28 through 47 removed outlier: 4.425A pdb=" N LEU e 32 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS e 33 " --> pdb=" O LEU e 29 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER e 34 " --> pdb=" O GLU e 30 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS e 35 " --> pdb=" O ALA e 31 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET e 37 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL e 42 " --> pdb=" O ALA e 38 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR e 45 " --> pdb=" O ALA e 41 " (cutoff:3.500A) Processing helix chain 'e' and resid 71 through 79 Processing helix chain 'e' and resid 83 through 100 removed outlier: 3.515A pdb=" N LEU e 88 " --> pdb=" O GLN e 84 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET e 89 " --> pdb=" O ILE e 85 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL e 90 " --> pdb=" O ALA e 86 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU e 91 " --> pdb=" O LYS e 87 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU e 92 " --> pdb=" O LEU e 88 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER e 93 " --> pdb=" O MET e 89 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS e 94 " --> pdb=" O VAL e 90 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER e 95 " --> pdb=" O GLU e 91 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASP e 98 " --> pdb=" O LYS e 94 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU e 99 " --> pdb=" O SER e 95 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 123 removed outlier: 3.559A pdb=" N VAL e 107 " --> pdb=" O GLY e 103 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL e 108 " --> pdb=" O THR e 104 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN e 120 " --> pdb=" O GLU e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 149 removed outlier: 3.601A pdb=" N ILE e 131 " --> pdb=" O HIS e 127 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG e 140 " --> pdb=" O GLU e 136 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL e 141 " --> pdb=" O GLN e 137 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS e 148 " --> pdb=" O GLU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 160 through 171 removed outlier: 3.580A pdb=" N ILE e 164 " --> pdb=" O THR e 160 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN e 165 " --> pdb=" O GLU e 161 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR e 169 " --> pdb=" O GLN e 165 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR e 170 " --> pdb=" O THR e 166 " (cutoff:3.500A) Processing helix chain 'e' and resid 172 through 178 removed outlier: 6.045A pdb=" N VAL e 175 " --> pdb=" O GLY e 172 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL e 176 " --> pdb=" O SER e 173 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN e 177 " --> pdb=" O LYS e 174 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER e 178 " --> pdb=" O VAL e 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 172 through 178' Processing helix chain 'e' and resid 179 through 195 removed outlier: 3.716A pdb=" N MET e 183 " --> pdb=" O CYS e 179 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE e 186 " --> pdb=" O GLN e 182 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL e 194 " --> pdb=" O ALA e 190 " (cutoff:3.500A) Processing helix chain 'e' and resid 216 through 220 removed outlier: 3.683A pdb=" N THR e 220 " --> pdb=" O LEU e 217 " (cutoff:3.500A) Processing helix chain 'e' and resid 268 through 294 removed outlier: 3.642A pdb=" N ALA e 274 " --> pdb=" O GLU e 270 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS e 277 " --> pdb=" O LYS e 273 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE e 287 " --> pdb=" O PHE e 283 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN e 288 " --> pdb=" O GLU e 284 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE e 290 " --> pdb=" O MET e 286 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS e 291 " --> pdb=" O ILE e 287 " (cutoff:3.500A) Processing helix chain 'e' and resid 305 through 316 removed outlier: 3.935A pdb=" N LEU e 311 " --> pdb=" O GLU e 307 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU e 312 " --> pdb=" O ALA e 308 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN e 314 " --> pdb=" O HIS e 310 " (cutoff:3.500A) Processing helix chain 'e' and resid 326 through 335 removed outlier: 3.659A pdb=" N LEU e 330 " --> pdb=" O PRO e 326 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE e 331 " --> pdb=" O GLU e 327 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA e 332 " --> pdb=" O ILE e 328 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE e 333 " --> pdb=" O GLU e 329 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA e 334 " --> pdb=" O LEU e 330 " (cutoff:3.500A) Processing helix chain 'e' and resid 389 through 413 removed outlier: 3.654A pdb=" N ARG e 398 " --> pdb=" O GLU e 394 " (cutoff:3.500A) Processing helix chain 'e' and resid 421 through 436 removed outlier: 3.523A pdb=" N ILE e 425 " --> pdb=" O GLY e 421 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU e 429 " --> pdb=" O ILE e 425 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP e 436 " --> pdb=" O SER e 432 " (cutoff:3.500A) Processing helix chain 'e' and resid 442 through 454 Processing helix chain 'e' and resid 454 through 464 removed outlier: 3.574A pdb=" N LEU e 460 " --> pdb=" O ILE e 456 " (cutoff:3.500A) Processing helix chain 'e' and resid 467 through 479 removed outlier: 3.669A pdb=" N GLU e 474 " --> pdb=" O GLN e 470 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL e 475 " --> pdb=" O THR e 471 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG e 476 " --> pdb=" O MET e 472 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA e 477 " --> pdb=" O THR e 473 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG e 478 " --> pdb=" O GLU e 474 " (cutoff:3.500A) Processing helix chain 'e' and resid 508 through 527 removed outlier: 3.767A pdb=" N LYS e 527 " --> pdb=" O ARG e 523 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 37 removed outlier: 3.586A pdb=" N ASN g 26 " --> pdb=" O VAL g 22 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE g 27 " --> pdb=" O GLN g 23 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE g 33 " --> pdb=" O ALA g 29 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 70 removed outlier: 3.502A pdb=" N LEU g 67 " --> pdb=" O GLY g 63 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG g 68 " --> pdb=" O ASN g 64 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 91 removed outlier: 3.860A pdb=" N MET g 80 " --> pdb=" O ALA g 76 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE g 81 " --> pdb=" O ALA g 77 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR g 86 " --> pdb=" O GLU g 82 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU g 90 " --> pdb=" O THR g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 94 through 106 removed outlier: 3.663A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU g 106 " --> pdb=" O ALA g 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.616A pdb=" N VAL g 122 " --> pdb=" O HIS g 118 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP g 131 " --> pdb=" O ARG g 127 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP g 132 " --> pdb=" O LYS g 128 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER g 135 " --> pdb=" O ASP g 131 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE g 140 " --> pdb=" O THR g 136 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 161 removed outlier: 3.597A pdb=" N ASN g 154 " --> pdb=" O ASP g 150 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE g 155 " --> pdb=" O MET g 151 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER g 158 " --> pdb=" O ASN g 154 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N SER g 159 " --> pdb=" O ILE g 155 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE g 160 " --> pdb=" O ILE g 156 " (cutoff:3.500A) Processing helix chain 'g' and resid 163 through 167 removed outlier: 3.597A pdb=" N SER g 166 " --> pdb=" O LYS g 163 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 163 through 167' Processing helix chain 'g' and resid 168 through 184 removed outlier: 3.750A pdb=" N VAL g 180 " --> pdb=" O ALA g 176 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS g 181 " --> pdb=" O LEU g 177 " (cutoff:3.500A) Processing helix chain 'g' and resid 194 through 198 Processing helix chain 'g' and resid 208 through 212 Processing helix chain 'g' and resid 270 through 281 removed outlier: 3.884A pdb=" N TYR g 274 " --> pdb=" O MET g 270 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE g 275 " --> pdb=" O GLU g 271 " (cutoff:3.500A) Processing helix chain 'g' and resid 299 through 307 removed outlier: 3.858A pdb=" N TYR g 303 " --> pdb=" O LEU g 299 " (cutoff:3.500A) Processing helix chain 'g' and resid 316 through 327 removed outlier: 3.548A pdb=" N ARG g 322 " --> pdb=" O THR g 318 " (cutoff:3.500A) Processing helix chain 'g' and resid 380 through 404 removed outlier: 3.561A pdb=" N ARG g 389 " --> pdb=" O SER g 385 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN g 392 " --> pdb=" O GLU g 388 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL g 397 " --> pdb=" O ASP g 393 " (cutoff:3.500A) Processing helix chain 'g' and resid 412 through 427 removed outlier: 3.636A pdb=" N MET g 416 " --> pdb=" O GLY g 412 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA g 421 " --> pdb=" O ALA g 417 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU g 424 " --> pdb=" O HIS g 420 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) Processing helix chain 'g' and resid 433 through 444 removed outlier: 3.535A pdb=" N VAL g 440 " --> pdb=" O PRO g 436 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA g 441 " --> pdb=" O TYR g 437 " (cutoff:3.500A) Processing helix chain 'g' and resid 445 through 456 Processing helix chain 'g' and resid 458 through 473 removed outlier: 3.810A pdb=" N ALA g 468 " --> pdb=" O THR g 464 " (cutoff:3.500A) Processing helix chain 'g' and resid 499 through 518 removed outlier: 3.520A pdb=" N ALA g 513 " --> pdb=" O ALA g 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 106 removed outlier: 3.948A pdb=" N LEU G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 140 removed outlier: 3.612A pdb=" N VAL G 122 " --> pdb=" O HIS G 118 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER G 135 " --> pdb=" O ASP G 131 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS G 138 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS G 139 " --> pdb=" O SER G 135 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE G 140 " --> pdb=" O THR G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 161 removed outlier: 3.579A pdb=" N ILE G 155 " --> pdb=" O MET G 151 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER G 158 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE G 160 " --> pdb=" O ILE G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 167 removed outlier: 4.113A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 removed outlier: 3.831A pdb=" N ASN G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL G 180 " --> pdb=" O ALA G 176 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS G 181 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL G 183 " --> pdb=" O ALA G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 189 removed outlier: 3.710A pdb=" N ASN G 188 " --> pdb=" O PHE G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 199 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 268 through 285 removed outlier: 3.588A pdb=" N GLU G 273 " --> pdb=" O GLN G 269 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU G 278 " --> pdb=" O TYR G 274 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP G 281 " --> pdb=" O GLN G 277 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE G 282 " --> pdb=" O LEU G 278 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 307 removed outlier: 3.509A pdb=" N GLN G 301 " --> pdb=" O SER G 297 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS G 302 " --> pdb=" O ASP G 298 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU G 304 " --> pdb=" O ALA G 300 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG G 306 " --> pdb=" O HIS G 302 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 327 removed outlier: 3.961A pdb=" N ARG G 322 " --> pdb=" O THR G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 404 removed outlier: 3.557A pdb=" N ASN G 390 " --> pdb=" O GLU G 386 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP G 393 " --> pdb=" O ARG G 389 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA G 394 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN G 396 " --> pdb=" O GLN G 392 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU G 403 " --> pdb=" O ARG G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 429 removed outlier: 3.592A pdb=" N GLU G 424 " --> pdb=" O HIS G 420 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER G 426 " --> pdb=" O LEU G 422 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 445 removed outlier: 3.632A pdb=" N ALA G 439 " --> pdb=" O TRP G 435 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL G 440 " --> pdb=" O PRO G 436 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA G 441 " --> pdb=" O TYR G 437 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN G 442 " --> pdb=" O ARG G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'G' and resid 458 through 472 removed outlier: 3.533A pdb=" N LEU G 462 " --> pdb=" O SER G 458 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS G 470 " --> pdb=" O LEU G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 518 removed outlier: 3.587A pdb=" N LYS G 507 " --> pdb=" O LEU G 503 " (cutoff:3.500A) Processing helix chain 'h' and resid 18 through 36 removed outlier: 3.650A pdb=" N LEU h 22 " --> pdb=" O GLY h 18 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL h 31 " --> pdb=" O SER h 27 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 37 through 40 removed outlier: 4.091A pdb=" N LEU h 40 " --> pdb=" O ARG h 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 37 through 40' Processing helix chain 'h' and resid 61 through 70 removed outlier: 3.812A pdb=" N ASP h 70 " --> pdb=" O LEU h 66 " (cutoff:3.500A) Processing helix chain 'h' and resid 73 through 90 removed outlier: 4.118A pdb=" N LEU h 79 " --> pdb=" O ALA h 75 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP h 87 " --> pdb=" O ALA h 83 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA h 88 " --> pdb=" O LYS h 84 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 108 removed outlier: 3.729A pdb=" N VAL h 97 " --> pdb=" O GLY h 93 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE h 104 " --> pdb=" O LEU h 100 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU h 105 " --> pdb=" O ALA h 101 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL h 108 " --> pdb=" O PHE h 104 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 3.629A pdb=" N GLU h 113 " --> pdb=" O LYS h 109 " (cutoff:3.500A) Processing helix chain 'h' and resid 117 through 140 removed outlier: 4.268A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE h 122 " --> pdb=" O PRO h 118 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG h 123 " --> pdb=" O GLN h 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR h 127 " --> pdb=" O ARG h 123 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS h 137 " --> pdb=" O VAL h 133 " (cutoff:3.500A) Processing helix chain 'h' and resid 145 through 149 Processing helix chain 'h' and resid 150 through 163 removed outlier: 3.572A pdb=" N GLU h 156 " --> pdb=" O ARG h 152 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR h 161 " --> pdb=" O LYS h 157 " (cutoff:3.500A) Processing helix chain 'h' and resid 171 through 185 removed outlier: 4.030A pdb=" N LYS h 177 " --> pdb=" O ALA h 173 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET h 178 " --> pdb=" O PHE h 174 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL h 180 " --> pdb=" O ALA h 176 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL h 183 " --> pdb=" O VAL h 179 " (cutoff:3.500A) Processing helix chain 'h' and resid 204 through 208 removed outlier: 3.632A pdb=" N SER h 208 " --> pdb=" O LEU h 205 " (cutoff:3.500A) Processing helix chain 'h' and resid 259 through 285 removed outlier: 3.592A pdb=" N TYR h 263 " --> pdb=" O THR h 259 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN h 264 " --> pdb=" O VAL h 260 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA h 265 " --> pdb=" O GLU h 261 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL h 267 " --> pdb=" O TYR h 263 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU h 274 " --> pdb=" O GLU h 270 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE h 281 " --> pdb=" O LYS h 277 " (cutoff:3.500A) Processing helix chain 'h' and resid 296 through 306 removed outlier: 3.644A pdb=" N GLN h 301 " --> pdb=" O ASP h 297 " (cutoff:3.500A) Processing helix chain 'h' and resid 315 through 327 removed outlier: 3.691A pdb=" N LEU h 319 " --> pdb=" O PRO h 315 " (cutoff:3.500A) Processing helix chain 'h' and resid 352 through 356 Processing helix chain 'h' and resid 378 through 402 removed outlier: 3.510A pdb=" N MET h 382 " --> pdb=" O ALA h 378 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU h 384 " --> pdb=" O GLN h 380 " (cutoff:3.500A) Processing helix chain 'h' and resid 410 through 426 removed outlier: 3.931A pdb=" N MET h 414 " --> pdb=" O GLY h 410 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU h 415 " --> pdb=" O ALA h 411 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 431 through 442 Processing helix chain 'h' and resid 443 through 453 removed outlier: 3.947A pdb=" N CYS h 450 " --> pdb=" O PRO h 446 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP h 451 " --> pdb=" O ARG h 447 " (cutoff:3.500A) Processing helix chain 'h' and resid 456 through 471 removed outlier: 3.807A pdb=" N ALA h 466 " --> pdb=" O ASN h 462 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG h 467 " --> pdb=" O LYS h 463 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS h 468 " --> pdb=" O LEU h 464 " (cutoff:3.500A) Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'H' and resid 19 through 36 removed outlier: 4.222A pdb=" N ILE H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 40 removed outlier: 4.191A pdb=" N LEU H 40 " --> pdb=" O ARG H 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 37 through 40' Processing helix chain 'H' and resid 61 through 70 removed outlier: 3.508A pdb=" N LEU H 66 " --> pdb=" O GLY H 62 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU H 68 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP H 70 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 90 removed outlier: 4.499A pdb=" N LEU H 79 " --> pdb=" O ALA H 75 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 108 removed outlier: 3.710A pdb=" N VAL H 97 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL H 108 " --> pdb=" O PHE H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 removed outlier: 3.566A pdb=" N GLU H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 140 removed outlier: 4.034A pdb=" N ILE H 121 " --> pdb=" O HIS H 117 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE H 122 " --> pdb=" O PRO H 118 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 149 removed outlier: 3.504A pdb=" N LYS H 148 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL H 149 " --> pdb=" O ALA H 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 145 through 149' Processing helix chain 'H' and resid 150 through 164 removed outlier: 3.580A pdb=" N THR H 161 " --> pdb=" O LYS H 157 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA H 162 " --> pdb=" O CYS H 158 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU H 163 " --> pdb=" O ALA H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 185 removed outlier: 3.511A pdb=" N PHE H 175 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET H 178 " --> pdb=" O PHE H 174 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL H 179 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 285 removed outlier: 3.946A pdb=" N GLN H 264 " --> pdb=" O VAL H 260 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP H 271 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS H 277 " --> pdb=" O ILE H 273 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS H 280 " --> pdb=" O ASP H 276 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE H 281 " --> pdb=" O LYS H 277 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY H 285 " --> pdb=" O ILE H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 removed outlier: 3.758A pdb=" N GLN H 301 " --> pdb=" O ASP H 297 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR H 302 " --> pdb=" O VAL H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 352 through 356 Processing helix chain 'H' and resid 378 through 402 removed outlier: 4.078A pdb=" N MET H 382 " --> pdb=" O ALA H 378 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU H 383 " --> pdb=" O GLU H 379 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS H 390 " --> pdb=" O GLU H 386 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP H 391 " --> pdb=" O ARG H 387 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET H 394 " --> pdb=" O HIS H 390 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE H 400 " --> pdb=" O VAL H 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 425 removed outlier: 3.658A pdb=" N MET H 414 " --> pdb=" O GLY H 410 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU H 416 " --> pdb=" O ILE H 412 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS H 418 " --> pdb=" O MET H 414 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG H 421 " --> pdb=" O SER H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 442 removed outlier: 3.949A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS H 440 " --> pdb=" O GLY H 436 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU H 442 " --> pdb=" O TYR H 438 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 452 Processing helix chain 'H' and resid 456 through 470 removed outlier: 3.926A pdb=" N ALA H 466 " --> pdb=" O ASN H 462 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS H 468 " --> pdb=" O LEU H 464 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA H 469 " --> pdb=" O ARG H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 515 removed outlier: 3.703A pdb=" N ILE H 513 " --> pdb=" O ALA H 509 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 45 removed outlier: 3.808A pdb=" N LEU Q 39 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN Q 41 " --> pdb=" O LYS Q 37 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR Q 42 " --> pdb=" O GLU Q 38 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 removed outlier: 3.540A pdb=" N ARG Q 74 " --> pdb=" O ALA Q 70 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 93 removed outlier: 3.976A pdb=" N MET Q 85 " --> pdb=" O PRO Q 81 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 122 removed outlier: 3.621A pdb=" N ALA Q 108 " --> pdb=" O VAL Q 104 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU Q 118 " --> pdb=" O LEU Q 114 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE Q 121 " --> pdb=" O GLU Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 143 removed outlier: 3.664A pdb=" N VAL Q 128 " --> pdb=" O SER Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 147 Processing helix chain 'Q' and resid 156 through 164 Processing helix chain 'Q' and resid 164 through 169 removed outlier: 3.652A pdb=" N ILE Q 168 " --> pdb=" O LEU Q 164 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N MET Q 169 " --> pdb=" O ARG Q 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 164 through 169' Processing helix chain 'Q' and resid 175 through 189 removed outlier: 3.575A pdb=" N LEU Q 179 " --> pdb=" O ASN Q 175 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS Q 181 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA Q 184 " --> pdb=" O ALA Q 180 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER Q 189 " --> pdb=" O GLN Q 185 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 215 removed outlier: 3.760A pdb=" N SER Q 214 " --> pdb=" O GLY Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 274 through 286 Processing helix chain 'Q' and resid 298 through 308 removed outlier: 3.627A pdb=" N HIS Q 303 " --> pdb=" O ASP Q 299 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA Q 305 " --> pdb=" O ALA Q 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN Q 306 " --> pdb=" O LEU Q 302 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR Q 308 " --> pdb=" O TYR Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 317 through 326 removed outlier: 3.599A pdb=" N LEU Q 321 " --> pdb=" O SER Q 317 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU Q 324 " --> pdb=" O ASP Q 320 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS Q 325 " --> pdb=" O LEU Q 321 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS Q 326 " --> pdb=" O ARG Q 322 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 403 removed outlier: 3.537A pdb=" N ASP Q 387 " --> pdb=" O ASN Q 383 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE Q 399 " --> pdb=" O GLY Q 395 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL Q 401 " --> pdb=" O ASN Q 397 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU Q 402 " --> pdb=" O THR Q 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 413 through 430 removed outlier: 3.590A pdb=" N ILE Q 417 " --> pdb=" O GLY Q 413 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN Q 422 " --> pdb=" O GLU Q 418 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER Q 425 " --> pdb=" O LYS Q 421 " (cutoff:3.500A) Processing helix chain 'Q' and resid 434 through 446 removed outlier: 3.688A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU Q 446 " --> pdb=" O ALA Q 442 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 456 Processing helix chain 'Q' and resid 459 through 473 removed outlier: 3.555A pdb=" N VAL Q 463 " --> pdb=" O LYS Q 459 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS Q 471 " --> pdb=" O LEU Q 467 " (cutoff:3.500A) Processing helix chain 'Q' and resid 492 through 496 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'q' and resid 29 through 45 removed outlier: 3.534A pdb=" N THR q 42 " --> pdb=" O GLU q 38 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 76 removed outlier: 3.637A pdb=" N ILE q 72 " --> pdb=" O ASP q 68 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU q 73 " --> pdb=" O ALA q 69 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG q 74 " --> pdb=" O ALA q 70 " (cutoff:3.500A) Processing helix chain 'q' and resid 80 through 93 removed outlier: 3.542A pdb=" N LYS q 84 " --> pdb=" O HIS q 80 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET q 85 " --> pdb=" O PRO q 81 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE q 86 " --> pdb=" O ALA q 82 " (cutoff:3.500A) Processing helix chain 'q' and resid 100 through 122 removed outlier: 3.616A pdb=" N ALA q 108 " --> pdb=" O VAL q 104 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU q 117 " --> pdb=" O GLU q 113 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE q 121 " --> pdb=" O GLU q 117 " (cutoff:3.500A) Processing helix chain 'q' and resid 124 through 143 removed outlier: 3.844A pdb=" N VAL q 128 " --> pdb=" O SER q 124 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG q 137 " --> pdb=" O GLU q 133 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU q 141 " --> pdb=" O ARG q 137 " (cutoff:3.500A) Processing helix chain 'q' and resid 144 through 147 Processing helix chain 'q' and resid 156 through 164 Processing helix chain 'q' and resid 164 through 169 Processing helix chain 'q' and resid 177 through 188 removed outlier: 3.997A pdb=" N LYS q 181 " --> pdb=" O VAL q 177 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA q 184 " --> pdb=" O ALA q 180 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA q 186 " --> pdb=" O LEU q 182 " (cutoff:3.500A) Processing helix chain 'q' and resid 198 through 200 No H-bonds generated for 'chain 'q' and resid 198 through 200' Processing helix chain 'q' and resid 211 through 215 removed outlier: 3.575A pdb=" N SER q 214 " --> pdb=" O GLY q 211 " (cutoff:3.500A) Processing helix chain 'q' and resid 263 through 287 removed outlier: 3.506A pdb=" N PHE q 268 " --> pdb=" O GLU q 264 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU q 273 " --> pdb=" O SER q 269 " (cutoff:3.500A) Processing helix chain 'q' and resid 298 through 308 removed outlier: 3.576A pdb=" N LEU q 302 " --> pdb=" O ALA q 298 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS q 303 " --> pdb=" O ASP q 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN q 306 " --> pdb=" O LEU q 302 " (cutoff:3.500A) Processing helix chain 'q' and resid 317 through 326 removed outlier: 3.780A pdb=" N LEU q 324 " --> pdb=" O ASP q 320 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS q 325 " --> pdb=" O LEU q 321 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS q 326 " --> pdb=" O ARG q 322 " (cutoff:3.500A) Processing helix chain 'q' and resid 381 through 402 removed outlier: 3.615A pdb=" N PHE q 399 " --> pdb=" O GLY q 395 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU q 402 " --> pdb=" O THR q 398 " (cutoff:3.500A) Processing helix chain 'q' and resid 414 through 430 removed outlier: 3.526A pdb=" N SER q 425 " --> pdb=" O LYS q 421 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 434 through 456 removed outlier: 3.502A pdb=" N GLU q 443 " --> pdb=" O LYS q 439 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU q 446 " --> pdb=" O ALA q 442 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA q 447 " --> pdb=" O GLU q 443 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE q 448 " --> pdb=" O ALA q 444 " (cutoff:3.500A) Proline residue: q 449 - end of helix Processing helix chain 'q' and resid 459 through 473 removed outlier: 3.549A pdb=" N VAL q 463 " --> pdb=" O LYS q 459 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS q 471 " --> pdb=" O LEU q 467 " (cutoff:3.500A) Processing helix chain 'q' and resid 492 through 496 Processing helix chain 'q' and resid 501 through 520 removed outlier: 3.896A pdb=" N TRP q 506 " --> pdb=" O LEU q 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 35 removed outlier: 3.925A pdb=" N ASN Z 23 " --> pdb=" O ALA Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 61 through 66 removed outlier: 3.642A pdb=" N GLU Z 66 " --> pdb=" O VAL Z 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 88 removed outlier: 3.768A pdb=" N ILE Z 77 " --> pdb=" O THR Z 73 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS Z 79 " --> pdb=" O SER Z 75 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL Z 80 " --> pdb=" O LEU Z 76 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP Z 86 " --> pdb=" O THR Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 91 through 111 removed outlier: 3.632A pdb=" N VAL Z 96 " --> pdb=" O THR Z 92 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU Z 108 " --> pdb=" O LYS Z 104 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.923A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU Z 135 " --> pdb=" O LEU Z 131 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU Z 136 " --> pdb=" O GLN Z 132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 157 removed outlier: 3.665A pdb=" N ASP Z 150 " --> pdb=" O GLU Z 146 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR Z 154 " --> pdb=" O ASP Z 150 " (cutoff:3.500A) Processing helix chain 'Z' and resid 158 through 160 No H-bonds generated for 'chain 'Z' and resid 158 through 160' Processing helix chain 'Z' and resid 164 through 179 removed outlier: 3.841A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE Z 179 " --> pdb=" O SER Z 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 189 No H-bonds generated for 'chain 'Z' and resid 187 through 189' Processing helix chain 'Z' and resid 252 through 264 removed outlier: 3.614A pdb=" N LYS Z 258 " --> pdb=" O GLU Z 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU Z 259 " --> pdb=" O GLU Z 255 " (cutoff:3.500A) Processing helix chain 'Z' and resid 264 through 281 removed outlier: 3.594A pdb=" N ASP Z 269 " --> pdb=" O LYS Z 265 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL Z 271 " --> pdb=" O ILE Z 267 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS Z 272 " --> pdb=" O GLU Z 268 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE Z 274 " --> pdb=" O ARG Z 270 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 307 removed outlier: 3.528A pdb=" N LYS Z 307 " --> pdb=" O ASP Z 303 " (cutoff:3.500A) Processing helix chain 'Z' and resid 317 through 329 removed outlier: 3.554A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU Z 326 " --> pdb=" O GLU Z 322 " (cutoff:3.500A) Processing helix chain 'Z' and resid 335 through 339 Processing helix chain 'Z' and resid 340 through 344 removed outlier: 3.754A pdb=" N CYS Z 343 " --> pdb=" O SER Z 340 " (cutoff:3.500A) Processing helix chain 'Z' and resid 380 through 404 removed outlier: 3.511A pdb=" N GLN Z 386 " --> pdb=" O HIS Z 382 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG Z 392 " --> pdb=" O LYS Z 388 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA Z 397 " --> pdb=" O ASP Z 393 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL Z 398 " --> pdb=" O GLY Z 394 " (cutoff:3.500A) Processing helix chain 'Z' and resid 412 through 424 removed outlier: 3.770A pdb=" N VAL Z 416 " --> pdb=" O GLY Z 412 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA Z 417 " --> pdb=" O ALA Z 413 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU Z 420 " --> pdb=" O VAL Z 416 " (cutoff:3.500A) Processing helix chain 'Z' and resid 433 through 445 removed outlier: 3.594A pdb=" N VAL Z 437 " --> pdb=" O ALA Z 433 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU Z 445 " --> pdb=" O ALA Z 441 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 455 removed outlier: 3.527A pdb=" N GLN Z 453 " --> pdb=" O LYS Z 449 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 469 removed outlier: 3.633A pdb=" N THR Z 462 " --> pdb=" O ASP Z 458 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU Z 463 " --> pdb=" O LEU Z 459 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS Z 465 " --> pdb=" O GLU Z 461 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE Z 466 " --> pdb=" O THR Z 462 " (cutoff:3.500A) Processing helix chain 'Z' and resid 488 through 493 Processing helix chain 'Z' and resid 498 through 517 removed outlier: 3.817A pdb=" N THR Z 509 " --> pdb=" O LEU Z 505 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL Z 510 " --> pdb=" O HIS Z 506 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU Z 517 " --> pdb=" O THR Z 513 " (cutoff:3.500A) Processing helix chain 'z' and resid 18 through 34 removed outlier: 3.649A pdb=" N VAL z 22 " --> pdb=" O ALA z 18 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN z 23 " --> pdb=" O ALA z 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU z 30 " --> pdb=" O ALA z 26 " (cutoff:3.500A) Processing helix chain 'z' and resid 61 through 66 removed outlier: 3.978A pdb=" N GLU z 66 " --> pdb=" O VAL z 62 " (cutoff:3.500A) Processing helix chain 'z' and resid 71 through 86 removed outlier: 3.684A pdb=" N SER z 75 " --> pdb=" O HIS z 71 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU z 76 " --> pdb=" O PRO z 72 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE z 77 " --> pdb=" O THR z 73 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS z 79 " --> pdb=" O SER z 75 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL z 80 " --> pdb=" O LEU z 76 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA z 81 " --> pdb=" O ILE z 77 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR z 82 " --> pdb=" O ALA z 78 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP z 86 " --> pdb=" O THR z 82 " (cutoff:3.500A) Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.564A pdb=" N VAL z 96 " --> pdb=" O THR z 92 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU z 97 " --> pdb=" O THR z 93 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU z 108 " --> pdb=" O LYS z 104 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.834A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU z 128 " --> pdb=" O GLU z 124 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU z 135 " --> pdb=" O LEU z 131 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU z 136 " --> pdb=" O GLN z 132 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL z 137 " --> pdb=" O PHE z 133 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS z 138 " --> pdb=" O LEU z 134 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 157 removed outlier: 3.830A pdb=" N ASP z 150 " --> pdb=" O GLU z 146 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR z 154 " --> pdb=" O ASP z 150 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG z 157 " --> pdb=" O ARG z 153 " (cutoff:3.500A) Processing helix chain 'z' and resid 158 through 160 No H-bonds generated for 'chain 'z' and resid 158 through 160' Processing helix chain 'z' and resid 164 through 178 removed outlier: 3.849A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA z 171 " --> pdb=" O VAL z 167 " (cutoff:3.500A) Processing helix chain 'z' and resid 187 through 189 No H-bonds generated for 'chain 'z' and resid 187 through 189' Processing helix chain 'z' and resid 200 through 204 removed outlier: 3.656A pdb=" N ASP z 203 " --> pdb=" O SER z 200 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR z 204 " --> pdb=" O GLU z 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 200 through 204' Processing helix chain 'z' and resid 252 through 281 removed outlier: 3.545A pdb=" N ARG z 256 " --> pdb=" O SER z 252 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU z 257 " --> pdb=" O ALA z 253 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS z 258 " --> pdb=" O GLU z 254 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA z 262 " --> pdb=" O LYS z 258 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE z 266 " --> pdb=" O ALA z 262 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS z 273 " --> pdb=" O ASP z 269 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE z 274 " --> pdb=" O ARG z 270 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE z 275 " --> pdb=" O VAL z 271 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 307 removed outlier: 3.730A pdb=" N LYS z 307 " --> pdb=" O ASP z 303 " (cutoff:3.500A) Processing helix chain 'z' and resid 317 through 329 removed outlier: 3.665A pdb=" N LEU z 326 " --> pdb=" O GLU z 322 " (cutoff:3.500A) Processing helix chain 'z' and resid 335 through 339 Processing helix chain 'z' and resid 340 through 344 removed outlier: 3.697A pdb=" N CYS z 343 " --> pdb=" O SER z 340 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU z 344 " --> pdb=" O PRO z 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 340 through 344' Processing helix chain 'z' and resid 380 through 404 removed outlier: 3.676A pdb=" N ALA z 397 " --> pdb=" O ASP z 393 " (cutoff:3.500A) Processing helix chain 'z' and resid 412 through 424 removed outlier: 3.642A pdb=" N LYS z 424 " --> pdb=" O GLU z 420 " (cutoff:3.500A) Processing helix chain 'z' and resid 433 through 445 removed outlier: 3.658A pdb=" N LEU z 445 " --> pdb=" O ALA z 441 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.584A pdb=" N LYS z 449 " --> pdb=" O LEU z 445 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN z 453 " --> pdb=" O LYS z 449 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 468 removed outlier: 3.895A pdb=" N LEU z 463 " --> pdb=" O LEU z 459 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE z 466 " --> pdb=" O THR z 462 " (cutoff:3.500A) Processing helix chain 'z' and resid 498 through 517 removed outlier: 3.541A pdb=" N HIS z 506 " --> pdb=" O LYS z 502 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR z 509 " --> pdb=" O LEU z 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.602A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASP g 521 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 137 through 138 Processing sheet with id=AA3, first strand: chain 'a' and resid 196 through 201 Processing sheet with id=AA4, first strand: chain 'a' and resid 215 through 216 removed outlier: 3.749A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 234 through 237 Processing sheet with id=AA6, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.572A pdb=" N ASP a 489 " --> pdb=" O LYS a 494 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS a 494 " --> pdb=" O ASP a 489 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 527 through 531 removed outlier: 4.274A pdb=" N ILE a 527 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE a 531 " --> pdb=" O GLN d 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS d 59 " --> pdb=" O THR d 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.665A pdb=" N THR A 55 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 43 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASP A 42 " --> pdb=" O ASP G 521 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N VAL G 523 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N MET A 44 " --> pdb=" O VAL G 523 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.690A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 209 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 215 through 216 removed outlier: 3.951A pdb=" N LEU A 361 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 234 through 237 removed outlier: 6.223A pdb=" N ILE A 286 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 408 through 410 Processing sheet with id=AB4, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.548A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.570A pdb=" N ILE D 61 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 62 through 64 removed outlier: 7.536A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR d 538 " --> pdb=" O ILE b 51 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU b 53 " --> pdb=" O THR d 538 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 199 through 204 removed outlier: 6.351A pdb=" N HIS b 200 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU b 375 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ILE b 202 " --> pdb=" O LEU b 375 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 233 through 235 removed outlier: 7.628A pdb=" N GLU b 233 " --> pdb=" O LEU b 348 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU b 348 " --> pdb=" O GLU b 233 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 237 through 240 removed outlier: 6.742A pdb=" N LEU b 238 " --> pdb=" O ILE b 291 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE b 290 " --> pdb=" O ILE b 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'b' and resid 406 through 407 Processing sheet with id=AC2, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AC3, first strand: chain 'b' and resid 517 through 522 removed outlier: 4.263A pdb=" N VAL b 517 " --> pdb=" O ASP e 56 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N MET e 58 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASN b 519 " --> pdb=" O MET e 58 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N VAL e 60 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE b 521 " --> pdb=" O VAL e 60 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR e 69 " --> pdb=" O LYS e 57 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR e 67 " --> pdb=" O MET e 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 62 through 64 removed outlier: 3.521A pdb=" N LEU B 52 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 406 through 408 Processing sheet with id=AC6, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AC7, first strand: chain 'B' and resid 520 through 522 Processing sheet with id=AC8, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC9, first strand: chain 'D' and resid 209 through 214 removed outlier: 6.673A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LYS D 213 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 240 through 244 removed outlier: 7.100A pdb=" N ARG D 240 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLU D 363 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLU D 242 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU D 361 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 246 through 248 removed outlier: 3.859A pdb=" N GLY D 247 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU D 299 " --> pdb=" O GLY D 247 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 491 through 494 Processing sheet with id=AD4, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AD5, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.484A pdb=" N LYS d 209 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL d 390 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL d 211 " --> pdb=" O VAL d 390 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N GLY d 392 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LYS d 213 " --> pdb=" O GLY d 392 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.517A pdb=" N LEU d 229 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU d 367 " --> pdb=" O GLY d 371 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU d 373 " --> pdb=" O VAL d 365 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU d 361 " --> pdb=" O THR d 377 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU d 360 " --> pdb=" O LYS d 243 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS d 243 " --> pdb=" O GLU d 360 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 246 through 248 Processing sheet with id=AD8, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AD9, first strand: chain 'E' and resid 207 through 211 removed outlier: 6.601A pdb=" N LYS E 208 " --> pdb=" O ILE E 383 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE E 385 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU E 210 " --> pdb=" O ILE E 385 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 225 through 228 removed outlier: 6.212A pdb=" N ASP E 367 " --> pdb=" O PHE E 362 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE E 362 " --> pdb=" O ASP E 367 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE E 360 " --> pdb=" O MET E 369 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 319 through 320 removed outlier: 6.945A pdb=" N ALA E 298 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL E 340 " --> pdb=" O ILE E 246 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE E 248 " --> pdb=" O VAL E 340 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 416 through 418 removed outlier: 3.832A pdb=" N VAL E 417 " --> pdb=" O GLU E 506 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU E 506 " --> pdb=" O VAL E 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 528 through 532 removed outlier: 7.149A pdb=" N ASP H 46 " --> pdb=" O ILE E 528 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ASP E 530 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU H 48 " --> pdb=" O ASP E 530 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'e' and resid 207 through 213 removed outlier: 3.525A pdb=" N LYS e 208 " --> pdb=" O VAL e 381 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY e 387 " --> pdb=" O LYS e 212 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'e' and resid 225 through 228 removed outlier: 3.729A pdb=" N VAL e 226 " --> pdb=" O ILE e 372 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE e 372 " --> pdb=" O VAL e 226 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL e 228 " --> pdb=" O LEU e 370 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP e 367 " --> pdb=" O PHE e 362 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N PHE e 362 " --> pdb=" O ASP e 367 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET e 369 " --> pdb=" O ILE e 360 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE e 360 " --> pdb=" O MET e 369 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'e' and resid 246 through 248 removed outlier: 6.746A pdb=" N ALA e 298 " --> pdb=" O VAL e 320 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'e' and resid 416 through 417 Processing sheet with id=AE9, first strand: chain 'e' and resid 528 through 532 removed outlier: 4.167A pdb=" N ILE e 528 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU h 48 " --> pdb=" O ILE e 528 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP e 530 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N VAL h 50 " --> pdb=" O ASP e 530 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG e 532 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'g' and resid 57 through 58 removed outlier: 6.814A pdb=" N MET g 47 " --> pdb=" O VAL z 518 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLU z 520 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET g 49 " --> pdb=" O GLU z 520 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'g' and resid 199 through 205 removed outlier: 4.170A pdb=" N ARG g 200 " --> pdb=" O CYS g 372 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE g 374 " --> pdb=" O ARG g 200 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU g 202 " --> pdb=" O ILE g 374 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'g' and resid 219 through 220 Processing sheet with id=AF4, first strand: chain 'g' and resid 232 through 233 Processing sheet with id=AF5, first strand: chain 'g' and resid 238 through 241 removed outlier: 5.983A pdb=" N VAL g 239 " --> pdb=" O ILE g 291 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 407 through 409 Processing sheet with id=AF7, first strand: chain 'G' and resid 142 through 143 removed outlier: 3.630A pdb=" N ILE G 142 " --> pdb=" O LEU G 407 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 202 through 205 removed outlier: 7.019A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 219 through 220 removed outlier: 3.545A pdb=" N THR G 361 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 232 through 233 removed outlier: 3.687A pdb=" N ILE G 233 " --> pdb=" O LEU G 350 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 238 through 240 Processing sheet with id=AG3, first strand: chain 'G' and resid 479 through 480 Processing sheet with id=AG4, first strand: chain 'h' and resid 15 through 16 removed outlier: 3.538A pdb=" N SER h 16 " --> pdb=" O THR h 519 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN q 53 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU h 518 " --> pdb=" O ASN q 53 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'h' and resid 141 through 142 removed outlier: 3.518A pdb=" N VAL h 405 " --> pdb=" O VAL h 141 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'h' and resid 195 through 201 removed outlier: 4.174A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'h' and resid 214 through 215 removed outlier: 3.671A pdb=" N VAL h 214 " --> pdb=" O PHE h 361 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE h 361 " --> pdb=" O VAL h 214 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'h' and resid 237 through 240 removed outlier: 3.609A pdb=" N LEU h 240 " --> pdb=" O SER h 290 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL h 289 " --> pdb=" O ALA h 311 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'h' and resid 475 through 477 Processing sheet with id=AH1, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AH2, first strand: chain 'H' and resid 195 through 199 removed outlier: 3.591A pdb=" N ILE H 373 " --> pdb=" O GLN H 209 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 214 through 215 removed outlier: 3.630A pdb=" N VAL H 214 " --> pdb=" O PHE H 361 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR H 358 " --> pdb=" O THR H 351 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE H 360 " --> pdb=" O GLU H 349 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 237 through 240 Processing sheet with id=AH5, first strand: chain 'H' and resid 475 through 477 Processing sheet with id=AH6, first strand: chain 'H' and resid 516 through 521 removed outlier: 6.626A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Q' and resid 202 through 208 Processing sheet with id=AH8, first strand: chain 'Q' and resid 221 through 223 removed outlier: 3.521A pdb=" N MET Q 221 " --> pdb=" O PHE Q 363 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL Q 361 " --> pdb=" O PHE Q 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR Q 351 " --> pdb=" O VAL Q 362 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Q' and resid 238 through 242 removed outlier: 7.293A pdb=" N LYS Q 238 " --> pdb=" O ALA Q 288 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL Q 290 " --> pdb=" O LYS Q 238 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASN Q 289 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL Q 313 " --> pdb=" O ASN Q 289 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL Q 291 " --> pdb=" O VAL Q 313 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 408 through 410 Processing sheet with id=AI2, first strand: chain 'Q' and resid 478 through 480 removed outlier: 3.787A pdb=" N LYS Q 490 " --> pdb=" O GLY Q 479 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Q' and resid 521 through 526 removed outlier: 4.376A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS Z 45 " --> pdb=" O THR Z 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR Z 57 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'q' and resid 202 through 208 removed outlier: 3.706A pdb=" N ILE q 375 " --> pdb=" O ARG q 203 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'q' and resid 221 through 223 removed outlier: 3.548A pdb=" N LYS q 364 " --> pdb=" O SER q 349 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER q 349 " --> pdb=" O LYS q 364 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'q' and resid 239 through 242 Processing sheet with id=AI7, first strand: chain 'q' and resid 408 through 409 Processing sheet with id=AI8, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AI9, first strand: chain 'q' and resid 521 through 526 removed outlier: 4.353A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.578A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'Z' and resid 211 through 212 removed outlier: 3.606A pdb=" N THR Z 361 " --> pdb=" O LEU Z 212 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Z' and resid 229 through 231 Processing sheet with id=AJ4, first strand: chain 'Z' and resid 407 through 409 removed outlier: 3.593A pdb=" N VAL Z 408 " --> pdb=" O ASP Z 496 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Z' and resid 478 through 479 Processing sheet with id=AJ6, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.784A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR z 373 " --> pdb=" O ILE z 207 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'z' and resid 224 through 225 removed outlier: 3.552A pdb=" N PHE z 360 " --> pdb=" O TYR z 353 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'z' and resid 229 through 231 removed outlier: 5.855A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ8 Processing sheet with id=AJ9, first strand: chain 'z' and resid 407 through 408 Processing sheet with id=AK1, first strand: chain 'z' and resid 477 through 479 2751 hydrogen bonds defined for protein. 8019 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: 27.80 Time building geometry restraints manager: 13.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 19776 1.34 - 1.46: 9959 1.46 - 1.58: 28864 1.58 - 1.69: 18 1.69 - 1.81: 599 Bond restraints: 59216 Sorted by residual: bond pdb=" C4' ADP Q 601 " pdb=" O4' ADP Q 601 " ideal model delta sigma weight residual 1.426 1.481 -0.055 2.00e-02 2.50e+03 7.68e+00 bond pdb=" C1' ADP Q 601 " pdb=" O4' ADP Q 601 " ideal model delta sigma weight residual 1.426 1.470 -0.044 2.00e-02 2.50e+03 4.94e+00 bond pdb=" C6 ADP Z 601 " pdb=" N1 ADP Z 601 " ideal model delta sigma weight residual 1.350 1.393 -0.043 2.00e-02 2.50e+03 4.68e+00 bond pdb=" C2 ADP Z 601 " pdb=" N1 ADP Z 601 " ideal model delta sigma weight residual 1.337 1.376 -0.039 2.00e-02 2.50e+03 3.86e+00 bond pdb=" CD1 TYR Q 47 " pdb=" CE1 TYR Q 47 " ideal model delta sigma weight residual 1.382 1.438 -0.056 3.00e-02 1.11e+03 3.44e+00 ... (remaining 59211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 78945 1.83 - 3.67: 746 3.67 - 5.50: 214 5.50 - 7.33: 40 7.33 - 9.17: 3 Bond angle restraints: 79948 Sorted by residual: angle pdb=" CA VAL a 409 " pdb=" C VAL a 409 " pdb=" N PRO a 410 " ideal model delta sigma weight residual 116.57 120.19 -3.62 9.80e-01 1.04e+00 1.36e+01 angle pdb=" N ASP A 358 " pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " ideal model delta sigma weight residual 114.17 110.02 4.15 1.14e+00 7.69e-01 1.32e+01 angle pdb=" C SER D 234 " pdb=" N ASN D 235 " pdb=" CA ASN D 235 " ideal model delta sigma weight residual 121.70 127.81 -6.11 1.80e+00 3.09e-01 1.15e+01 angle pdb=" N ILE Q 417 " pdb=" CA ILE Q 417 " pdb=" C ILE Q 417 " ideal model delta sigma weight residual 111.58 108.17 3.41 1.06e+00 8.90e-01 1.04e+01 angle pdb=" CA VAL g 408 " pdb=" C VAL g 408 " pdb=" N PRO g 409 " ideal model delta sigma weight residual 116.57 119.59 -3.02 9.80e-01 1.04e+00 9.51e+00 ... (remaining 79943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 35537 23.61 - 47.22: 1010 47.22 - 70.83: 119 70.83 - 94.44: 29 94.44 - 118.06: 4 Dihedral angle restraints: 36699 sinusoidal: 14672 harmonic: 22027 Sorted by residual: dihedral pdb=" CA ASP a 146 " pdb=" C ASP a 146 " pdb=" N CYS a 147 " pdb=" CA CYS a 147 " ideal model delta harmonic sigma weight residual 180.00 121.01 58.99 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA GLN A 187 " pdb=" C GLN A 187 " pdb=" N PRO A 188 " pdb=" CA PRO A 188 " ideal model delta harmonic sigma weight residual 180.00 -126.56 -53.44 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA GLN a 187 " pdb=" C GLN a 187 " pdb=" N PRO a 188 " pdb=" CA PRO a 188 " ideal model delta harmonic sigma weight residual -180.00 -126.80 -53.20 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 36696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 9581 0.132 - 0.264: 28 0.264 - 0.397: 0 0.397 - 0.529: 0 0.529 - 0.661: 1 Chirality restraints: 9610 Sorted by residual: chirality pdb=" C4' ADP Q 601 " pdb=" C3' ADP Q 601 " pdb=" C5' ADP Q 601 " pdb=" O4' ADP Q 601 " both_signs ideal model delta sigma weight residual False -2.50 -3.16 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CG LEU Z 481 " pdb=" CB LEU Z 481 " pdb=" CD1 LEU Z 481 " pdb=" CD2 LEU Z 481 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CA ILE g 204 " pdb=" N ILE g 204 " pdb=" C ILE g 204 " pdb=" CB ILE g 204 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 9607 not shown) Planarity restraints: 10225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN a 187 " 0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO a 188 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO a 188 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO a 188 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' ADP Z 601 " 0.010 2.00e-02 2.50e+03 1.69e-02 7.90e+00 pdb=" C2 ADP Z 601 " -0.027 2.00e-02 2.50e+03 pdb=" C4 ADP Z 601 " -0.002 2.00e-02 2.50e+03 pdb=" C5 ADP Z 601 " -0.009 2.00e-02 2.50e+03 pdb=" C6 ADP Z 601 " -0.013 2.00e-02 2.50e+03 pdb=" C8 ADP Z 601 " 0.005 2.00e-02 2.50e+03 pdb=" N1 ADP Z 601 " 0.044 2.00e-02 2.50e+03 pdb=" N3 ADP Z 601 " 0.000 2.00e-02 2.50e+03 pdb=" N6 ADP Z 601 " -0.005 2.00e-02 2.50e+03 pdb=" N7 ADP Z 601 " 0.004 2.00e-02 2.50e+03 pdb=" N9 ADP Z 601 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 187 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO A 188 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.036 5.00e-02 4.00e+02 ... (remaining 10222 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 470 2.60 - 3.17: 49009 3.17 - 3.75: 86190 3.75 - 4.32: 123137 4.32 - 4.90: 199190 Nonbonded interactions: 457996 Sorted by model distance: nonbonded pdb=" OG SER q 170 " pdb=" O2A ADP q 601 " model vdw 2.022 3.040 nonbonded pdb=" O ALA Z 165 " pdb=" OG1 THR Z 169 " model vdw 2.078 3.040 nonbonded pdb=" O GLY A 213 " pdb=" OG SER A 374 " model vdw 2.089 3.040 nonbonded pdb=" O LYS e 512 " pdb=" OG SER e 516 " model vdw 2.111 3.040 nonbonded pdb=" N TYR a 190 " pdb=" OE2 GLU a 404 " model vdw 2.121 3.120 ... (remaining 457991 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' selection = (chain 'a' and (resid 14 through 237 or resid 282 through 533)) } ncs_group { reference = (chain 'E' and resid 25 through 534) selection = chain 'e' } ncs_group { reference = chain 'H' selection = (chain 'h' and resid 18 through 524) } ncs_group { reference = chain 'Q' selection = (chain 'q' and (resid 28 through 242 or resid 273 through 529 or resid 601)) } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 17 through 525 or resid 601)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.070 Extract box with map and model: 1.680 Check model and map are aligned: 0.330 Set scattering table: 0.410 Process input model: 112.650 Find NCS groups from input model: 3.810 Set up NCS constraints: 0.330 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5115 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 : 0.003 0.056 59216 Z= 0.200 Angle : 0.580 9.167 79948 Z= 0.321 Chirality : 0.041 0.661 9610 Planarity : 0.003 0.074 10225 Dihedral : 11.642 118.055 22419 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.78 % Favored : 97.21 % Rotamer: Outliers : 0.06 % Allowed : 1.19 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.98 % Twisted General : 0.03 % 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: -4.27 (0.07), residues: 7598 helix: -3.34 (0.05), residues: 3667 sheet: -2.48 (0.18), residues: 617 loop : -2.08 (0.09), residues: 3314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP q 319 HIS 0.003 0.000 HIS Z 161 PHE 0.017 0.001 PHE e 362 TYR 0.011 0.001 TYR Q 47 ARG 0.004 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1728 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1724 time to evaluate : 4.814 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: 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: 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: 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 146 ASP cc_start: 0.7581 (t0) cc_final: 0.7376 (t0) REVERT: a 233 LYS cc_start: 0.3401 (mtmm) cc_final: 0.3131 (mtmm) REVERT: a 421 ILE cc_start: 0.7059 (mm) cc_final: 0.6581 (mm) REVERT: A 133 ASN cc_start: 0.6885 (m-40) cc_final: 0.6558 (t0) REVERT: A 344 MET cc_start: 0.2917 (mtt) cc_final: 0.2647 (mpp) REVERT: A 528 ASP cc_start: 0.5710 (t0) cc_final: 0.5330 (t0) REVERT: b 66 ASP cc_start: 0.6758 (t70) cc_final: 0.6362 (t70) REVERT: b 112 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6716 (mm-30) REVERT: b 135 LYS cc_start: 0.8212 (mmtm) cc_final: 0.7976 (ptmm) REVERT: b 203 LYS cc_start: 0.5236 (mtmt) cc_final: 0.4378 (mtpt) REVERT: b 228 GLN cc_start: 0.2568 (mm-40) cc_final: 0.2168 (mt0) REVERT: b 275 MET cc_start: 0.3400 (mmt) cc_final: 0.3200 (mmt) REVERT: b 460 ASP cc_start: 0.7329 (m-30) cc_final: 0.7064 (m-30) REVERT: B 112 GLU cc_start: 0.6897 (tp30) cc_final: 0.6680 (tp30) REVERT: B 484 THR cc_start: 0.3431 (t) cc_final: 0.1871 (t) REVERT: B 521 ILE cc_start: 0.7410 (mt) cc_final: 0.6835 (mt) REVERT: D 90 MET cc_start: 0.7124 (mtm) cc_final: 0.6769 (mtp) REVERT: D 98 GLN cc_start: 0.7710 (tp40) cc_final: 0.7327 (tp40) REVERT: D 148 LEU cc_start: 0.7228 (mt) cc_final: 0.6869 (tt) REVERT: D 320 MET cc_start: -0.1757 (mmt) cc_final: -0.2265 (ptp) REVERT: D 345 VAL cc_start: 0.2487 (t) cc_final: 0.2166 (t) REVERT: D 385 THR cc_start: 0.2291 (p) cc_final: 0.1336 (p) REVERT: D 446 MET cc_start: 0.5282 (mtt) cc_final: 0.4397 (mmm) REVERT: D 479 GLU cc_start: 0.5966 (tt0) cc_final: 0.5591 (tp30) REVERT: D 512 LEU cc_start: 0.5153 (tp) cc_final: 0.4007 (tp) REVERT: d 52 LEU cc_start: 0.6560 (tp) cc_final: 0.6254 (tp) REVERT: d 211 VAL cc_start: 0.4992 (t) cc_final: 0.4548 (m) REVERT: d 415 LEU cc_start: 0.7878 (mt) cc_final: 0.7279 (tp) REVERT: E 66 VAL cc_start: 0.5355 (t) cc_final: 0.4596 (m) REVERT: E 75 ILE cc_start: 0.6635 (mt) cc_final: 0.6390 (mt) REVERT: E 205 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6744 (mt-10) REVERT: E 216 ARG cc_start: 0.6298 (mmt-90) cc_final: 0.5696 (mpp-170) REVERT: E 345 GLU cc_start: 0.5091 (mm-30) cc_final: 0.4412 (mp0) REVERT: E 366 LYS cc_start: -0.0316 (tmtt) cc_final: -0.0763 (ptmm) REVERT: E 369 MET cc_start: 0.3048 (mtp) cc_final: 0.2646 (mtm) REVERT: E 484 ASN cc_start: 0.5454 (m-40) cc_final: 0.5234 (m-40) REVERT: E 491 CYS cc_start: 0.7889 (p) cc_final: 0.7474 (p) REVERT: E 521 MET cc_start: 0.6470 (tpt) cc_final: 0.4781 (ttm) REVERT: e 26 LEU cc_start: 0.7794 (mp) cc_final: 0.7000 (tp) REVERT: e 30 GLU cc_start: 0.7245 (mp0) cc_final: 0.5982 (pt0) REVERT: e 46 MET cc_start: 0.6502 (mtp) cc_final: 0.6022 (mmp) REVERT: e 59 MET cc_start: 0.7341 (mmp) cc_final: 0.6964 (mmp) REVERT: e 63 ASP cc_start: 0.6030 (m-30) cc_final: 0.5468 (m-30) REVERT: e 78 MET cc_start: 0.7797 (tpt) cc_final: 0.7319 (tpt) REVERT: e 117 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6553 (mm-30) REVERT: e 296 ASN cc_start: 0.5439 (m-40) cc_final: 0.4393 (t0) REVERT: e 345 GLU cc_start: 0.4632 (mm-30) cc_final: 0.3885 (pt0) REVERT: e 456 ILE cc_start: 0.8358 (mt) cc_final: 0.7790 (mt) REVERT: e 513 GLN cc_start: 0.6616 (mm-40) cc_final: 0.5914 (mm-40) REVERT: g 50 LEU cc_start: 0.8170 (mp) cc_final: 0.7536 (mp) REVERT: g 59 MET cc_start: 0.7062 (tpp) cc_final: 0.6666 (mmm) REVERT: g 78 LYS cc_start: 0.7395 (mttt) cc_final: 0.6766 (ttmt) REVERT: g 112 PHE cc_start: 0.4547 (m-80) cc_final: 0.3816 (m-80) REVERT: g 113 LEU cc_start: 0.7044 (mp) cc_final: 0.6838 (mp) REVERT: g 237 ARG cc_start: 0.7525 (mtt180) cc_final: 0.6728 (ttm-80) REVERT: G 153 LEU cc_start: 0.7418 (tp) cc_final: 0.7023 (tp) REVERT: G 157 ASN cc_start: 0.7551 (m-40) cc_final: 0.7122 (p0) REVERT: G 229 MET cc_start: 0.0490 (mtt) cc_final: 0.0278 (mtt) REVERT: G 305 MET cc_start: 0.3497 (mtm) cc_final: 0.3264 (tpp) REVERT: h 117 HIS cc_start: 0.6314 (t-90) cc_final: 0.5913 (t-90) REVERT: h 217 LYS cc_start: 0.4474 (tttt) cc_final: 0.3991 (mppt) REVERT: H 116 LEU cc_start: 0.7823 (tp) cc_final: 0.7206 (mm) REVERT: H 184 MET cc_start: 0.2802 (mtp) cc_final: 0.1250 (tpp) REVERT: H 418 LYS cc_start: 0.7429 (tttm) cc_final: 0.7092 (tmtt) REVERT: H 517 ASP cc_start: 0.6115 (m-30) cc_final: 0.5653 (m-30) REVERT: Q 92 MET cc_start: 0.7066 (mmm) cc_final: 0.6546 (mmp) REVERT: Q 153 ASN cc_start: 0.5912 (t0) cc_final: 0.5639 (t0) REVERT: Q 196 HIS cc_start: 0.5896 (m90) cc_final: 0.5461 (t70) REVERT: Q 318 LYS cc_start: 0.4690 (mttt) cc_final: 0.4175 (pptt) REVERT: Q 320 ASP cc_start: 0.4444 (m-30) cc_final: 0.3936 (m-30) REVERT: Q 388 ILE cc_start: 0.8851 (mt) cc_final: 0.8550 (tt) REVERT: Q 491 ASP cc_start: 0.6094 (t0) cc_final: 0.5454 (t70) REVERT: q 62 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7660 (tptm) REVERT: q 101 THR cc_start: 0.7576 (m) cc_final: 0.7333 (p) REVERT: q 315 LEU cc_start: 0.6384 (mt) cc_final: 0.5896 (tp) REVERT: q 385 MET cc_start: 0.4833 (ttp) cc_final: 0.4360 (ttp) REVERT: Z 71 HIS cc_start: 0.6114 (t-90) cc_final: 0.5859 (t-90) REVERT: Z 187 ASP cc_start: 0.1690 (t0) cc_final: 0.1034 (t0) REVERT: Z 355 LEU cc_start: 0.5935 (mt) cc_final: 0.5706 (mt) REVERT: Z 393 ASP cc_start: 0.5206 (m-30) cc_final: 0.4848 (m-30) REVERT: z 292 ILE cc_start: 0.3285 (pt) cc_final: 0.2674 (tp) REVERT: z 521 ILE cc_start: 0.7208 (mt) cc_final: 0.6873 (mp) outliers start: 4 outliers final: 1 residues processed: 1728 average time/residue: 0.5852 time to fit residues: 1662.0793 Evaluate side-chains 1008 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1007 time to evaluate : 4.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 640 optimal weight: 20.0000 chunk 575 optimal weight: 10.0000 chunk 319 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 388 optimal weight: 0.4980 chunk 307 optimal weight: 5.9990 chunk 594 optimal weight: 0.8980 chunk 230 optimal weight: 0.8980 chunk 361 optimal weight: 4.9990 chunk 442 optimal weight: 0.3980 chunk 689 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 103 ASN a 113 HIS a 425 ASN a 472 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN b 174 HIS b 361 HIS b 399 GLN B 122 HIS D 129 HIS d 347 HIS d 482 ASN E 296 ASN ** E 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 84 GLN g 308 ASN g 390 ASN g 392 GLN G 392 GLN G 420 HIS h 30 GLN h 86 GLN h 117 HIS h 390 HIS h 431 GLN h 432 GLN h 448 GLN H 130 GLN H 234 ASN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 HIS Q 102 ASN Q 365 HIS Q 477 ASN q 50 ASN q 91 HIS q 93 GLN q 477 ASN Z 23 ASN Z 161 HIS Z 245 ASN Z 434 GLN ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5216 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 59216 Z= 0.193 Angle : 0.597 9.988 79948 Z= 0.305 Chirality : 0.044 0.223 9610 Planarity : 0.004 0.075 10225 Dihedral : 4.521 94.394 8179 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.14 % Allowed : 3.00 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.98 % 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: -2.29 (0.08), residues: 7598 helix: -1.12 (0.07), residues: 3913 sheet: -2.01 (0.17), residues: 701 loop : -1.75 (0.10), residues: 2984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 493 HIS 0.013 0.001 HIS h 117 PHE 0.028 0.002 PHE H 303 TYR 0.020 0.001 TYR H 275 ARG 0.014 0.001 ARG q 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1353 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1344 time to evaluate : 5.054 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: 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: 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: 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 17 ILE cc_start: 0.6681 (mp) cc_final: 0.6187 (mp) REVERT: a 73 LYS cc_start: 0.7047 (mmtt) cc_final: 0.6276 (mmtt) REVERT: a 146 ASP cc_start: 0.7457 (t0) cc_final: 0.6909 (t0) REVERT: a 233 LYS cc_start: 0.3510 (mtmm) cc_final: 0.3103 (mtmm) REVERT: A 127 GLU cc_start: 0.3433 (mm-30) cc_final: 0.3038 (mm-30) REVERT: A 133 ASN cc_start: 0.6079 (m-40) cc_final: 0.5863 (t0) REVERT: A 209 MET cc_start: 0.3626 (mmt) cc_final: 0.3395 (mmt) REVERT: A 306 MET cc_start: 0.3777 (tpp) cc_final: 0.1853 (mtt) REVERT: A 344 MET cc_start: 0.2478 (mtt) cc_final: 0.2198 (mpp) REVERT: b 53 LEU cc_start: 0.7633 (pt) cc_final: 0.7149 (pp) REVERT: b 228 GLN cc_start: 0.2161 (mm-40) cc_final: 0.1540 (mt0) REVERT: b 275 MET cc_start: 0.3598 (mmt) cc_final: 0.3375 (mmt) REVERT: b 354 ILE cc_start: 0.4534 (mt) cc_final: 0.4260 (mt) REVERT: b 436 MET cc_start: 0.4916 (mtt) cc_final: 0.4327 (mmt) REVERT: b 460 ASP cc_start: 0.7449 (m-30) cc_final: 0.7065 (m-30) REVERT: B 78 ASN cc_start: 0.4072 (t0) cc_final: 0.3868 (m110) REVERT: B 119 LYS cc_start: 0.8734 (mmmt) cc_final: 0.7865 (tptp) REVERT: B 394 LEU cc_start: 0.3994 (mm) cc_final: 0.3767 (mm) REVERT: B 402 LYS cc_start: 0.8531 (tttt) cc_final: 0.8019 (mptt) REVERT: B 436 MET cc_start: 0.5647 (mtt) cc_final: 0.4941 (mmm) REVERT: B 445 MET cc_start: 0.6724 (mmm) cc_final: 0.6385 (tpt) REVERT: B 488 MET cc_start: 0.7628 (mmm) cc_final: 0.7347 (mmm) REVERT: D 79 LYS cc_start: 0.6358 (ptpt) cc_final: 0.6151 (ptpp) REVERT: D 81 MET cc_start: 0.6121 (mmm) cc_final: 0.5254 (mtt) REVERT: D 96 LYS cc_start: 0.7635 (mttt) cc_final: 0.7351 (tptt) REVERT: D 138 GLN cc_start: 0.4517 (pp30) cc_final: 0.3333 (pp30) REVERT: D 141 LEU cc_start: 0.6734 (pp) cc_final: 0.6507 (tt) REVERT: D 320 MET cc_start: -0.2629 (mmt) cc_final: -0.3036 (ptp) REVERT: D 345 VAL cc_start: 0.1269 (t) cc_final: 0.1013 (t) REVERT: D 364 GLU cc_start: 0.3505 (mt-10) cc_final: 0.2883 (pp20) REVERT: D 458 MET cc_start: 0.7718 (mpp) cc_final: 0.7362 (mpp) REVERT: D 459 GLU cc_start: 0.6451 (mt-10) cc_final: 0.6093 (tm-30) REVERT: D 479 GLU cc_start: 0.6323 (tt0) cc_final: 0.5936 (tp30) REVERT: D 512 LEU cc_start: 0.5002 (tp) cc_final: 0.3984 (tp) REVERT: d 109 VAL cc_start: 0.7853 (t) cc_final: 0.7611 (t) REVERT: d 192 MET cc_start: 0.5176 (mmp) cc_final: 0.4454 (tmm) REVERT: d 211 VAL cc_start: 0.5032 (t) cc_final: 0.4681 (m) REVERT: d 214 LEU cc_start: 0.6076 (pt) cc_final: 0.5171 (tt) REVERT: d 415 LEU cc_start: 0.7566 (mt) cc_final: 0.6971 (tp) REVERT: E 140 ARG cc_start: 0.7584 (mmp80) cc_final: 0.7240 (mmp80) REVERT: E 201 ASP cc_start: 0.3270 (m-30) cc_final: 0.2712 (m-30) REVERT: E 286 MET cc_start: 0.4617 (mmt) cc_final: 0.4256 (mmt) REVERT: E 369 MET cc_start: 0.3296 (mtp) cc_final: 0.2442 (mtm) REVERT: E 484 ASN cc_start: 0.5804 (m-40) cc_final: 0.5458 (m110) REVERT: E 491 CYS cc_start: 0.7868 (p) cc_final: 0.7514 (p) REVERT: E 521 MET cc_start: 0.5853 (OUTLIER) cc_final: 0.5541 (ttm) REVERT: e 30 GLU cc_start: 0.7476 (mp0) cc_final: 0.5546 (pt0) REVERT: e 79 MET cc_start: 0.6188 (mtm) cc_final: 0.5835 (mtm) REVERT: e 116 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6436 (tm-30) REVERT: e 119 GLU cc_start: 0.7677 (tt0) cc_final: 0.7448 (tt0) REVERT: e 296 ASN cc_start: 0.6534 (m-40) cc_final: 0.4982 (t0) REVERT: e 345 GLU cc_start: 0.3671 (mm-30) cc_final: 0.3174 (pt0) REVERT: g 490 MET cc_start: 0.4769 (tpp) cc_final: 0.4183 (tpp) REVERT: G 153 LEU cc_start: 0.7280 (tp) cc_final: 0.6545 (tp) REVERT: G 157 ASN cc_start: 0.7760 (m-40) cc_final: 0.7355 (p0) REVERT: G 416 MET cc_start: 0.5083 (mmm) cc_final: 0.4711 (mmm) REVERT: G 440 VAL cc_start: 0.7261 (t) cc_final: 0.7008 (t) REVERT: G 483 GLU cc_start: 0.6452 (mm-30) cc_final: 0.6120 (mp0) REVERT: h 111 TYR cc_start: 0.6024 (m-10) cc_final: 0.5640 (m-80) REVERT: h 217 LYS cc_start: 0.4637 (tttt) cc_final: 0.4009 (mppt) REVERT: h 324 MET cc_start: 0.4022 (ppp) cc_final: 0.1786 (mmm) REVERT: h 382 MET cc_start: -0.1484 (mtp) cc_final: -0.2298 (mmm) REVERT: h 383 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7566 (tt0) REVERT: h 500 ILE cc_start: 0.6428 (OUTLIER) cc_final: 0.6043 (tt) REVERT: H 216 PHE cc_start: 0.3024 (p90) cc_final: 0.2576 (p90) REVERT: H 309 PHE cc_start: 0.6298 (t80) cc_final: 0.5747 (t80) REVERT: H 318 ASP cc_start: 0.3933 (m-30) cc_final: 0.3309 (t0) REVERT: H 358 TYR cc_start: 0.3292 (m-80) cc_final: 0.2999 (m-80) REVERT: H 370 CYS cc_start: 0.5188 (p) cc_final: 0.4704 (p) REVERT: H 418 LYS cc_start: 0.7576 (tttm) cc_final: 0.7210 (tppt) REVERT: H 517 ASP cc_start: 0.5946 (m-30) cc_final: 0.5664 (m-30) REVERT: Q 52 MET cc_start: 0.4584 (mmt) cc_final: 0.4277 (mmt) REVERT: Q 63 LEU cc_start: 0.7353 (tp) cc_final: 0.7065 (tp) REVERT: Q 116 GLU cc_start: 0.6093 (mm-30) cc_final: 0.5071 (mm-30) REVERT: Q 153 ASN cc_start: 0.5941 (t0) cc_final: 0.5422 (t0) REVERT: Q 196 HIS cc_start: 0.5921 (m90) cc_final: 0.5142 (t70) REVERT: Q 320 ASP cc_start: 0.4497 (m-30) cc_final: 0.4165 (m-30) REVERT: Q 377 LEU cc_start: 0.8125 (tp) cc_final: 0.7710 (tp) REVERT: Q 419 LEU cc_start: 0.7171 (tp) cc_final: 0.6903 (tp) REVERT: q 62 LYS cc_start: 0.7753 (mmtt) cc_final: 0.7506 (tptm) REVERT: q 221 MET cc_start: 0.5053 (mtp) cc_final: 0.4741 (mtm) REVERT: q 315 LEU cc_start: 0.6660 (mt) cc_final: 0.6266 (tp) REVERT: q 415 THR cc_start: 0.5079 (p) cc_final: 0.4855 (p) REVERT: Z 385 THR cc_start: 0.7018 (m) cc_final: 0.6716 (m) REVERT: z 73 THR cc_start: 0.7518 (m) cc_final: 0.7294 (m) REVERT: z 208 ARG cc_start: 0.5037 (mmp80) cc_final: 0.4750 (mmp80) REVERT: z 370 ARG cc_start: 0.6770 (mtp-110) cc_final: 0.6339 (ttp-110) REVERT: z 385 THR cc_start: 0.7558 (m) cc_final: 0.7330 (p) outliers start: 9 outliers final: 2 residues processed: 1347 average time/residue: 0.5699 time to fit residues: 1298.2094 Evaluate side-chains 958 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 954 time to evaluate : 4.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 383 optimal weight: 0.4980 chunk 213 optimal weight: 3.9990 chunk 573 optimal weight: 0.9990 chunk 469 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 690 optimal weight: 7.9990 chunk 745 optimal weight: 1.9990 chunk 614 optimal weight: 4.9990 chunk 684 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 553 optimal weight: 5.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 21 ASN a 103 ASN a 113 HIS a 187 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 124 GLN b 161 ASN b 174 HIS B 122 HIS B 148 HIS B 178 HIS B 391 HIS B 419 HIS D 129 HIS E 316 ASN E 497 ASN E 514 GLN e 120 GLN ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 497 ASN ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 400 ASN g 420 HIS G 115 GLN h 30 GLN ** h 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 GLN H 468 HIS ** q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 196 HIS q 219 HIS Z 105 GLN ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 198 HIS Z 293 ASN z 105 GLN z 294 GLN z 320 ASN z 346 HIS z 382 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5367 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 59216 Z= 0.227 Angle : 0.632 11.637 79948 Z= 0.317 Chirality : 0.045 0.239 9610 Planarity : 0.004 0.084 10225 Dihedral : 4.754 88.211 8179 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.13 % Allowed : 3.55 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.98 % 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: -1.52 (0.09), residues: 7598 helix: -0.33 (0.08), residues: 3921 sheet: -1.76 (0.17), residues: 768 loop : -1.59 (0.11), residues: 2909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 493 HIS 0.008 0.001 HIS E 180 PHE 0.019 0.002 PHE q 103 TYR 0.022 0.002 TYR H 275 ARG 0.011 0.001 ARG D 435 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1218 time to evaluate : 5.053 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: 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: 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: 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 17 ILE cc_start: 0.6678 (mp) cc_final: 0.6386 (mp) REVERT: a 52 VAL cc_start: 0.8781 (t) cc_final: 0.8569 (p) REVERT: a 66 GLU cc_start: 0.7143 (tt0) cc_final: 0.6679 (mm-30) REVERT: a 73 LYS cc_start: 0.7386 (mmtt) cc_final: 0.6594 (mmtt) REVERT: a 187 GLN cc_start: 0.3770 (OUTLIER) cc_final: 0.3013 (tp-100) REVERT: a 225 MET cc_start: 0.0154 (mmt) cc_final: -0.0054 (mmt) REVERT: a 233 LYS cc_start: 0.3817 (mtmm) cc_final: 0.2805 (mttp) REVERT: A 344 MET cc_start: 0.2212 (mtt) cc_final: 0.1876 (mpp) REVERT: A 370 ARG cc_start: 0.2721 (ptt-90) cc_final: 0.1034 (ptt90) REVERT: A 498 ASN cc_start: 0.5258 (m110) cc_final: 0.4846 (t0) REVERT: b 48 MET cc_start: 0.6018 (mmp) cc_final: 0.5780 (mmt) REVERT: b 228 GLN cc_start: 0.0840 (mm-40) cc_final: 0.0589 (mt0) REVERT: b 275 MET cc_start: 0.3442 (mmt) cc_final: 0.3079 (mmt) REVERT: B 112 GLU cc_start: 0.7151 (tp30) cc_final: 0.6817 (tp30) REVERT: B 119 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8216 (pttm) REVERT: B 394 LEU cc_start: 0.3286 (mm) cc_final: 0.3077 (mm) REVERT: B 402 LYS cc_start: 0.8598 (tttt) cc_final: 0.8089 (mptt) REVERT: B 445 MET cc_start: 0.7057 (mmm) cc_final: 0.6738 (tpt) REVERT: D 79 LYS cc_start: 0.6525 (ptpt) cc_final: 0.6266 (ptpp) REVERT: D 80 GLN cc_start: 0.7891 (mp10) cc_final: 0.7663 (mp10) REVERT: D 141 LEU cc_start: 0.7051 (pp) cc_final: 0.6596 (tt) REVERT: D 320 MET cc_start: -0.2762 (mmt) cc_final: -0.3119 (ptp) REVERT: D 364 GLU cc_start: 0.3788 (mt-10) cc_final: 0.3002 (pp20) REVERT: D 446 MET cc_start: 0.5990 (mtt) cc_final: 0.5396 (mtp) REVERT: D 479 GLU cc_start: 0.6409 (tt0) cc_final: 0.6075 (tp30) REVERT: D 497 LYS cc_start: 0.7174 (tmtt) cc_final: 0.6895 (tttm) REVERT: d 129 HIS cc_start: 0.7378 (t-90) cc_final: 0.6565 (t70) REVERT: d 192 MET cc_start: 0.5025 (mmp) cc_final: 0.4226 (tmm) REVERT: d 211 VAL cc_start: 0.3860 (t) cc_final: 0.3476 (m) REVERT: d 214 LEU cc_start: 0.6002 (pt) cc_final: 0.5749 (pt) REVERT: d 282 TYR cc_start: 0.3161 (t80) cc_final: 0.1423 (m-80) REVERT: d 415 LEU cc_start: 0.7531 (mt) cc_final: 0.6799 (tp) REVERT: d 434 LEU cc_start: 0.7065 (tp) cc_final: 0.6770 (tp) REVERT: E 89 MET cc_start: 0.8694 (mpp) cc_final: 0.8068 (mpp) REVERT: E 204 PHE cc_start: 0.5957 (t80) cc_final: 0.5734 (t80) REVERT: E 369 MET cc_start: 0.2148 (mtp) cc_final: 0.1479 (mtm) REVERT: E 491 CYS cc_start: 0.7783 (p) cc_final: 0.7552 (p) REVERT: e 30 GLU cc_start: 0.7528 (mp0) cc_final: 0.5873 (pt0) REVERT: e 46 MET cc_start: 0.8252 (mmp) cc_final: 0.7338 (mmt) REVERT: e 63 ASP cc_start: 0.6304 (p0) cc_final: 0.5715 (p0) REVERT: e 78 MET cc_start: 0.8263 (tpt) cc_final: 0.7678 (tpt) REVERT: e 121 LEU cc_start: 0.8196 (mt) cc_final: 0.7994 (mt) REVERT: e 296 ASN cc_start: 0.6803 (m-40) cc_final: 0.5157 (t0) REVERT: e 345 GLU cc_start: 0.4055 (mm-30) cc_final: 0.3580 (pt0) REVERT: e 369 MET cc_start: -0.2536 (mtp) cc_final: -0.4479 (ptp) REVERT: g 112 PHE cc_start: 0.3886 (m-80) cc_final: 0.3002 (m-80) REVERT: g 237 ARG cc_start: 0.7704 (ttt90) cc_final: 0.6951 (ttm-80) REVERT: g 517 LEU cc_start: 0.7112 (mt) cc_final: 0.6797 (mt) REVERT: G 157 ASN cc_start: 0.7480 (m-40) cc_final: 0.7194 (p0) REVERT: G 416 MET cc_start: 0.5450 (mmm) cc_final: 0.5173 (mmm) REVERT: G 501 VAL cc_start: 0.7116 (t) cc_final: 0.6845 (t) REVERT: h 111 TYR cc_start: 0.6019 (m-10) cc_final: 0.5633 (m-80) REVERT: h 158 CYS cc_start: 0.4854 (m) cc_final: 0.3334 (m) REVERT: h 160 MET cc_start: 0.6188 (ppp) cc_final: 0.5909 (ppp) REVERT: h 217 LYS cc_start: 0.4571 (tttt) cc_final: 0.4037 (mttp) REVERT: h 460 ILE cc_start: 0.7415 (mt) cc_final: 0.7169 (mt) REVERT: h 500 ILE cc_start: 0.6266 (OUTLIER) cc_final: 0.5798 (tt) REVERT: H 216 PHE cc_start: 0.3105 (p90) cc_final: 0.2637 (p90) REVERT: H 318 ASP cc_start: 0.4213 (m-30) cc_final: 0.3442 (t70) REVERT: H 370 CYS cc_start: 0.5089 (p) cc_final: 0.4732 (p) REVERT: H 517 ASP cc_start: 0.5957 (m-30) cc_final: 0.5697 (m-30) REVERT: Q 153 ASN cc_start: 0.5572 (t0) cc_final: 0.4998 (t0) REVERT: Q 230 ASP cc_start: 0.5045 (t70) cc_final: 0.4661 (p0) REVERT: Q 377 LEU cc_start: 0.8234 (tp) cc_final: 0.7984 (tp) REVERT: Q 385 MET cc_start: 0.7516 (mmm) cc_final: 0.7017 (mmm) REVERT: Q 459 LYS cc_start: 0.7308 (mttt) cc_final: 0.7076 (mttp) REVERT: q 62 LYS cc_start: 0.7611 (mmtt) cc_final: 0.7337 (tptm) REVERT: q 315 LEU cc_start: 0.6914 (mt) cc_final: 0.6509 (tp) REVERT: q 320 ASP cc_start: 0.7523 (m-30) cc_final: 0.7075 (m-30) REVERT: q 454 GLU cc_start: 0.6552 (mm-30) cc_final: 0.5599 (mm-30) REVERT: Z 143 MET cc_start: 0.6103 (ppp) cc_final: 0.5526 (ppp) REVERT: Z 179 ILE cc_start: 0.5814 (pt) cc_final: 0.4092 (pt) REVERT: Z 344 LEU cc_start: 0.2422 (tt) cc_final: 0.1984 (mm) REVERT: Z 385 THR cc_start: 0.7068 (m) cc_final: 0.6755 (m) REVERT: z 196 MET cc_start: 0.5123 (mmm) cc_final: 0.4918 (mmm) REVERT: z 208 ARG cc_start: 0.5088 (mmp80) cc_final: 0.4797 (mmp80) REVERT: z 370 ARG cc_start: 0.6985 (mtp-110) cc_final: 0.6640 (ttp-110) outliers start: 8 outliers final: 0 residues processed: 1223 average time/residue: 0.5365 time to fit residues: 1122.7127 Evaluate side-chains 912 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 910 time to evaluate : 4.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 682 optimal weight: 1.9990 chunk 519 optimal weight: 2.9990 chunk 358 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 329 optimal weight: 0.9990 chunk 463 optimal weight: 0.9980 chunk 692 optimal weight: 6.9990 chunk 733 optimal weight: 0.9990 chunk 362 optimal weight: 1.9990 chunk 656 optimal weight: 10.0000 chunk 197 optimal weight: 9.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 21 ASN a 103 ASN a 133 ASN a 135 ASN a 251 GLN a 262 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 ASN ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 HIS ** E 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 497 ASN ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 301 GLN h 380 GLN h 431 GLN h 448 GLN H 134 ASN H 233 HIS H 282 HIS ** Q 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 435 GLN ** q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 105 GLN ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 346 HIS z 105 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5346 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 59216 Z= 0.177 Angle : 0.583 11.225 79948 Z= 0.289 Chirality : 0.043 0.185 9610 Planarity : 0.004 0.107 10225 Dihedral : 4.677 80.050 8179 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.98 % 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: -1.06 (0.09), residues: 7598 helix: 0.09 (0.08), residues: 3932 sheet: -1.60 (0.18), residues: 753 loop : -1.44 (0.11), residues: 2913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 493 HIS 0.009 0.001 HIS E 401 PHE 0.022 0.002 PHE Q 107 TYR 0.017 0.001 TYR h 438 ARG 0.010 0.000 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1164 time to evaluate : 5.084 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: 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: 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 66 GLU cc_start: 0.7145 (tt0) cc_final: 0.6753 (mm-30) REVERT: a 73 LYS cc_start: 0.7331 (mmtt) cc_final: 0.6580 (mmtt) REVERT: a 171 MET cc_start: 0.4459 (mmt) cc_final: 0.3446 (ptp) REVERT: a 206 MET cc_start: 0.5967 (mmm) cc_final: 0.5524 (mmm) REVERT: a 233 LYS cc_start: 0.3870 (mtmm) cc_final: 0.2827 (mttp) REVERT: a 345 LEU cc_start: 0.5460 (mt) cc_final: 0.5168 (mt) REVERT: a 384 MET cc_start: -0.0324 (ptm) cc_final: -0.0661 (ptm) REVERT: A 134 GLU cc_start: 0.6518 (pp20) cc_final: 0.6123 (pp20) REVERT: A 344 MET cc_start: 0.2284 (mtt) cc_final: 0.1933 (mpp) REVERT: A 370 ARG cc_start: 0.2554 (ptt-90) cc_final: 0.0878 (ptt90) REVERT: A 498 ASN cc_start: 0.5361 (m-40) cc_final: 0.4632 (t0) REVERT: b 35 ILE cc_start: 0.8851 (mm) cc_final: 0.8462 (tp) REVERT: b 105 LEU cc_start: 0.6874 (tp) cc_final: 0.6648 (tp) REVERT: b 275 MET cc_start: 0.3145 (mmt) cc_final: 0.2790 (mmt) REVERT: b 436 MET cc_start: 0.4613 (mtt) cc_final: 0.4205 (mmt) REVERT: B 112 GLU cc_start: 0.7034 (tp30) cc_final: 0.6680 (tp30) REVERT: B 119 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8041 (pttm) REVERT: B 402 LYS cc_start: 0.8619 (tttt) cc_final: 0.8170 (mptt) REVERT: B 436 MET cc_start: 0.5828 (mtt) cc_final: 0.5295 (mmm) REVERT: B 445 MET cc_start: 0.6914 (mmm) cc_final: 0.6630 (tpt) REVERT: B 488 MET cc_start: 0.6783 (mmm) cc_final: 0.6581 (mmm) REVERT: B 512 GLU cc_start: 0.6649 (pm20) cc_final: 0.5577 (pp20) REVERT: D 60 MET cc_start: 0.3738 (ptt) cc_final: 0.3488 (ptt) REVERT: D 79 LYS cc_start: 0.6469 (ptpt) cc_final: 0.6088 (pttt) REVERT: D 138 GLN cc_start: 0.4813 (pp30) cc_final: 0.4055 (pp30) REVERT: D 141 LEU cc_start: 0.7086 (pp) cc_final: 0.6614 (tt) REVERT: D 320 MET cc_start: -0.2887 (mmt) cc_final: -0.3244 (ptp) REVERT: D 364 GLU cc_start: 0.3829 (mt-10) cc_final: 0.3065 (pp20) REVERT: D 446 MET cc_start: 0.5880 (mtt) cc_final: 0.5178 (mtt) REVERT: D 479 GLU cc_start: 0.6347 (tt0) cc_final: 0.6047 (tp30) REVERT: d 96 LYS cc_start: 0.7139 (mmmt) cc_final: 0.6703 (mmmt) REVERT: d 128 ILE cc_start: 0.8288 (mp) cc_final: 0.7301 (mm) REVERT: d 129 HIS cc_start: 0.7239 (t-90) cc_final: 0.6710 (t70) REVERT: d 192 MET cc_start: 0.5580 (mmp) cc_final: 0.4721 (tmm) REVERT: d 211 VAL cc_start: 0.4681 (t) cc_final: 0.4317 (m) REVERT: d 214 LEU cc_start: 0.6078 (pt) cc_final: 0.5223 (tt) REVERT: d 282 TYR cc_start: 0.3138 (t80) cc_final: 0.1458 (m-10) REVERT: d 415 LEU cc_start: 0.7610 (mt) cc_final: 0.6857 (tp) REVERT: d 434 LEU cc_start: 0.7109 (tp) cc_final: 0.6861 (tp) REVERT: E 27 MET cc_start: 0.3736 (mtm) cc_final: 0.3286 (mtm) REVERT: E 201 ASP cc_start: 0.4838 (m-30) cc_final: 0.4628 (m-30) REVERT: E 286 MET cc_start: 0.4658 (mmt) cc_final: 0.4192 (mmt) REVERT: E 369 MET cc_start: 0.2222 (mtp) cc_final: 0.1451 (mtm) REVERT: E 446 MET cc_start: 0.7155 (mmt) cc_final: 0.6285 (mmt) REVERT: E 491 CYS cc_start: 0.7581 (p) cc_final: 0.7323 (p) REVERT: e 30 GLU cc_start: 0.7618 (mp0) cc_final: 0.5919 (pt0) REVERT: e 46 MET cc_start: 0.8175 (mmp) cc_final: 0.7122 (mmt) REVERT: e 78 MET cc_start: 0.8232 (tpt) cc_final: 0.8014 (tpt) REVERT: e 296 ASN cc_start: 0.6681 (m-40) cc_final: 0.4942 (t0) REVERT: e 345 GLU cc_start: 0.4155 (mm-30) cc_final: 0.3631 (pt0) REVERT: e 369 MET cc_start: -0.2710 (mtp) cc_final: -0.4426 (ptp) REVERT: g 112 PHE cc_start: 0.3940 (m-80) cc_final: 0.3194 (m-80) REVERT: g 192 GLU cc_start: 0.7171 (pp20) cc_final: 0.6628 (pp20) REVERT: g 237 ARG cc_start: 0.7654 (ttt90) cc_final: 0.6793 (ttm-80) REVERT: g 517 LEU cc_start: 0.7110 (mt) cc_final: 0.6674 (mt) REVERT: G 157 ASN cc_start: 0.7538 (m-40) cc_final: 0.7174 (p0) REVERT: h 45 MET cc_start: 0.6668 (mmm) cc_final: 0.6465 (mmm) REVERT: h 111 TYR cc_start: 0.5761 (m-10) cc_final: 0.5425 (m-80) REVERT: h 160 MET cc_start: 0.5725 (ppp) cc_final: 0.5385 (ppp) REVERT: h 217 LYS cc_start: 0.4530 (tttt) cc_final: 0.3996 (mttp) REVERT: h 251 ASP cc_start: 0.3448 (m-30) cc_final: 0.3162 (t0) REVERT: h 382 MET cc_start: -0.2277 (mtp) cc_final: -0.2942 (mmm) REVERT: h 448 GLN cc_start: 0.5289 (mm-40) cc_final: 0.4897 (mm-40) REVERT: h 460 ILE cc_start: 0.7367 (mt) cc_final: 0.6910 (mt) REVERT: H 100 LEU cc_start: 0.6940 (mt) cc_final: 0.6485 (mt) REVERT: H 106 LYS cc_start: 0.8476 (tppt) cc_final: 0.8213 (tppt) REVERT: H 211 VAL cc_start: 0.4326 (t) cc_final: 0.4122 (t) REVERT: H 216 PHE cc_start: 0.2932 (p90) cc_final: 0.2576 (p90) REVERT: H 318 ASP cc_start: 0.4212 (m-30) cc_final: 0.3422 (t70) REVERT: H 358 TYR cc_start: 0.4896 (m-80) cc_final: 0.4684 (m-80) REVERT: H 370 CYS cc_start: 0.5155 (p) cc_final: 0.4684 (p) REVERT: H 517 ASP cc_start: 0.6400 (m-30) cc_final: 0.6194 (m-30) REVERT: Q 52 MET cc_start: 0.4594 (mmm) cc_final: 0.4175 (mmt) REVERT: Q 153 ASN cc_start: 0.5470 (t0) cc_final: 0.5069 (t0) REVERT: Q 230 ASP cc_start: 0.5043 (t70) cc_final: 0.4597 (p0) REVERT: Q 377 LEU cc_start: 0.8053 (tp) cc_final: 0.7699 (tt) REVERT: q 62 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7316 (tptm) REVERT: q 221 MET cc_start: 0.5204 (mtt) cc_final: 0.4945 (mtt) REVERT: q 315 LEU cc_start: 0.6893 (mt) cc_final: 0.6566 (tp) REVERT: q 320 ASP cc_start: 0.7657 (m-30) cc_final: 0.7251 (m-30) REVERT: q 415 THR cc_start: 0.5297 (p) cc_final: 0.5030 (p) REVERT: q 454 GLU cc_start: 0.6437 (mm-30) cc_final: 0.5529 (mm-30) REVERT: Z 90 ASP cc_start: 0.4776 (t0) cc_final: 0.4133 (t0) REVERT: Z 385 THR cc_start: 0.7302 (m) cc_final: 0.7019 (m) REVERT: z 34 LEU cc_start: 0.7438 (mm) cc_final: 0.6996 (mt) REVERT: z 73 THR cc_start: 0.7811 (m) cc_final: 0.7601 (m) REVERT: z 208 ARG cc_start: 0.5117 (mmp80) cc_final: 0.4894 (mmp80) REVERT: z 321 MET cc_start: 0.4636 (mmp) cc_final: 0.4408 (mmm) REVERT: z 370 ARG cc_start: 0.7069 (mtp-110) cc_final: 0.6649 (ttp-110) outliers start: 3 outliers final: 0 residues processed: 1166 average time/residue: 0.5420 time to fit residues: 1087.7911 Evaluate side-chains 913 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 913 time to evaluate : 4.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 611 optimal weight: 3.9990 chunk 416 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 546 optimal weight: 2.9990 chunk 302 optimal weight: 9.9990 chunk 626 optimal weight: 0.0970 chunk 507 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 374 optimal weight: 0.1980 chunk 658 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 103 ASN a 482 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 HIS d 347 HIS ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS g 115 GLN g 154 ASN g 321 ASN ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 154 ASN G 420 HIS h 107 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 HIS ** Q 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 93 GLN q 185 GLN q 472 GLN q 523 GLN Z 105 GLN ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 59216 Z= 0.214 Angle : 0.612 10.535 79948 Z= 0.307 Chirality : 0.044 0.184 9610 Planarity : 0.004 0.095 10225 Dihedral : 4.757 72.340 8179 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.98 % 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: -1.00 (0.09), residues: 7598 helix: 0.15 (0.08), residues: 3951 sheet: -1.59 (0.18), residues: 760 loop : -1.41 (0.11), residues: 2887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 493 HIS 0.008 0.001 HIS H 390 PHE 0.028 0.002 PHE q 103 TYR 0.042 0.002 TYR H 275 ARG 0.010 0.001 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1134 time to evaluate : 4.958 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: 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: 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 66 GLU cc_start: 0.7140 (tt0) cc_final: 0.6816 (mm-30) REVERT: a 73 LYS cc_start: 0.7252 (mmtt) cc_final: 0.6732 (mmtt) REVERT: a 126 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8402 (tptt) REVERT: a 206 MET cc_start: 0.6068 (mmm) cc_final: 0.5051 (tmm) REVERT: A 127 GLU cc_start: 0.3317 (mm-30) cc_final: 0.2766 (mm-30) REVERT: A 134 GLU cc_start: 0.6683 (pp20) cc_final: 0.6440 (tm-30) REVERT: A 498 ASN cc_start: 0.5766 (m-40) cc_final: 0.4819 (t0) REVERT: b 35 ILE cc_start: 0.8833 (mm) cc_final: 0.8544 (tp) REVERT: b 275 MET cc_start: 0.3213 (mmt) cc_final: 0.2912 (mmt) REVERT: b 417 MET cc_start: 0.6313 (mtt) cc_final: 0.6084 (mtt) REVERT: B 112 GLU cc_start: 0.6946 (tp30) cc_final: 0.6529 (tp30) REVERT: B 119 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8176 (pttm) REVERT: B 402 LYS cc_start: 0.8643 (tttt) cc_final: 0.8221 (mptt) REVERT: B 436 MET cc_start: 0.5964 (mtt) cc_final: 0.5226 (mmm) REVERT: B 445 MET cc_start: 0.6970 (mmm) cc_final: 0.6643 (tpt) REVERT: B 512 GLU cc_start: 0.6467 (pm20) cc_final: 0.5981 (pp20) REVERT: D 138 GLN cc_start: 0.4835 (pp30) cc_final: 0.4223 (pp30) REVERT: D 141 LEU cc_start: 0.7161 (pp) cc_final: 0.6750 (tt) REVERT: D 364 GLU cc_start: 0.4020 (mt-10) cc_final: 0.2862 (pp20) REVERT: D 446 MET cc_start: 0.5710 (mtt) cc_final: 0.5205 (mtt) REVERT: D 458 MET cc_start: 0.8184 (mpp) cc_final: 0.7794 (mpp) REVERT: D 479 GLU cc_start: 0.6201 (tt0) cc_final: 0.5784 (tp30) REVERT: d 95 SER cc_start: 0.8020 (m) cc_final: 0.7786 (p) REVERT: d 128 ILE cc_start: 0.8179 (mp) cc_final: 0.7583 (mm) REVERT: d 129 HIS cc_start: 0.7222 (t-90) cc_final: 0.6810 (t-90) REVERT: d 192 MET cc_start: 0.5615 (mmp) cc_final: 0.4997 (tmm) REVERT: d 282 TYR cc_start: 0.2707 (t80) cc_final: 0.1047 (m-80) REVERT: d 415 LEU cc_start: 0.7654 (mt) cc_final: 0.7414 (tp) REVERT: d 434 LEU cc_start: 0.7066 (tp) cc_final: 0.6761 (tp) REVERT: d 523 THR cc_start: 0.8863 (m) cc_final: 0.8501 (p) REVERT: E 27 MET cc_start: 0.3123 (mtm) cc_final: 0.2683 (mtm) REVERT: E 79 MET cc_start: 0.5215 (ttt) cc_final: 0.4975 (ttt) REVERT: E 140 ARG cc_start: 0.7857 (mmp80) cc_final: 0.7639 (mmp80) REVERT: E 147 ASP cc_start: 0.8406 (m-30) cc_final: 0.7916 (m-30) REVERT: E 207 ILE cc_start: 0.2610 (mt) cc_final: 0.2106 (pt) REVERT: E 286 MET cc_start: 0.4920 (mmt) cc_final: 0.4539 (mmt) REVERT: E 369 MET cc_start: 0.2912 (mtp) cc_final: 0.2130 (mtm) REVERT: E 446 MET cc_start: 0.7442 (mmt) cc_final: 0.6549 (mmt) REVERT: E 491 CYS cc_start: 0.7474 (p) cc_final: 0.7195 (p) REVERT: e 30 GLU cc_start: 0.7680 (mp0) cc_final: 0.7396 (mp0) REVERT: e 46 MET cc_start: 0.8199 (mmp) cc_final: 0.7087 (mmt) REVERT: e 63 ASP cc_start: 0.5942 (p0) cc_final: 0.5722 (p0) REVERT: e 79 MET cc_start: 0.6097 (mtm) cc_final: 0.5715 (mtm) REVERT: e 345 GLU cc_start: 0.4604 (mm-30) cc_final: 0.3957 (pt0) REVERT: e 369 MET cc_start: -0.2553 (mtp) cc_final: -0.4356 (ptp) REVERT: g 112 PHE cc_start: 0.4013 (m-80) cc_final: 0.3458 (m-80) REVERT: g 237 ARG cc_start: 0.7682 (ttt90) cc_final: 0.7094 (ttm-80) REVERT: g 517 LEU cc_start: 0.7183 (mt) cc_final: 0.6924 (mt) REVERT: G 157 ASN cc_start: 0.7710 (m-40) cc_final: 0.7317 (p0) REVERT: G 219 MET cc_start: 0.1662 (mtm) cc_final: 0.0399 (ttm) REVERT: h 111 TYR cc_start: 0.5410 (m-10) cc_final: 0.4987 (m-80) REVERT: h 160 MET cc_start: 0.5784 (ppp) cc_final: 0.5426 (ppp) REVERT: h 217 LYS cc_start: 0.4511 (tttt) cc_final: 0.3965 (mttp) REVERT: h 448 GLN cc_start: 0.5368 (mm-40) cc_final: 0.5060 (mm-40) REVERT: h 460 ILE cc_start: 0.7471 (mt) cc_final: 0.7236 (mt) REVERT: h 520 ILE cc_start: 0.8244 (mm) cc_final: 0.7945 (mm) REVERT: H 211 VAL cc_start: 0.4359 (t) cc_final: 0.4097 (t) REVERT: H 216 PHE cc_start: 0.3350 (p90) cc_final: 0.3142 (p90) REVERT: H 318 ASP cc_start: 0.4259 (m-30) cc_final: 0.3601 (t70) REVERT: H 358 TYR cc_start: 0.4699 (m-80) cc_final: 0.4317 (m-80) REVERT: H 370 CYS cc_start: 0.4134 (p) cc_final: 0.3259 (p) REVERT: H 480 ASN cc_start: 0.7822 (m-40) cc_final: 0.7602 (m-40) REVERT: Q 153 ASN cc_start: 0.5573 (t0) cc_final: 0.5224 (t0) REVERT: Q 161 SER cc_start: 0.7740 (m) cc_final: 0.7141 (p) REVERT: Q 230 ASP cc_start: 0.4245 (t70) cc_final: 0.4017 (p0) REVERT: Q 238 LYS cc_start: 0.6647 (mmmt) cc_final: 0.6368 (tttm) REVERT: Q 351 TYR cc_start: 0.3998 (p90) cc_final: 0.3442 (p90) REVERT: q 62 LYS cc_start: 0.7802 (mmtt) cc_final: 0.7369 (tptm) REVERT: q 221 MET cc_start: 0.4801 (mtt) cc_final: 0.4368 (mtt) REVERT: q 315 LEU cc_start: 0.6940 (mt) cc_final: 0.6560 (tp) REVERT: q 320 ASP cc_start: 0.7753 (m-30) cc_final: 0.7374 (m-30) REVERT: q 438 ILE cc_start: 0.6669 (mm) cc_final: 0.6406 (mm) REVERT: q 454 GLU cc_start: 0.6542 (mm-30) cc_final: 0.5851 (mm-30) REVERT: Z 43 THR cc_start: 0.4538 (p) cc_final: 0.3965 (p) REVERT: Z 90 ASP cc_start: 0.4709 (t0) cc_final: 0.4046 (t0) REVERT: Z 179 ILE cc_start: 0.6080 (pt) cc_final: 0.5603 (pt) REVERT: Z 385 THR cc_start: 0.7355 (m) cc_final: 0.7066 (m) REVERT: z 208 ARG cc_start: 0.5323 (mmp80) cc_final: 0.5089 (mmp80) outliers start: 0 outliers final: 0 residues processed: 1134 average time/residue: 0.5435 time to fit residues: 1057.5282 Evaluate side-chains 887 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 887 time to evaluate : 4.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 246 optimal weight: 1.9990 chunk 660 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 chunk 430 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 734 optimal weight: 6.9990 chunk 609 optimal weight: 0.8980 chunk 340 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 385 optimal weight: 0.5980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 103 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN B 122 HIS B 399 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 HIS d 347 HIS ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS ** g 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 235 ASN H 60 ASN Q 175 ASN Q 201 ASN Q 461 ASN q 91 HIS ** q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 523 GLN Z 105 GLN ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 59216 Z= 0.197 Angle : 0.611 22.501 79948 Z= 0.304 Chirality : 0.044 0.253 9610 Planarity : 0.004 0.085 10225 Dihedral : 4.861 90.798 8179 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.02 % Allowed : 1.57 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.98 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.09), residues: 7598 helix: 0.25 (0.08), residues: 3956 sheet: -1.46 (0.18), residues: 737 loop : -1.37 (0.11), residues: 2905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP h 493 HIS 0.006 0.001 HIS z 218 PHE 0.026 0.002 PHE h 104 TYR 0.031 0.002 TYR H 275 ARG 0.008 0.000 ARG z 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1129 time to evaluate : 5.101 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: 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: 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: symmetry clash revert: symmetry clash REVERT: a 66 GLU cc_start: 0.7117 (tt0) cc_final: 0.6715 (mm-30) REVERT: a 73 LYS cc_start: 0.7238 (mmtt) cc_final: 0.6657 (mmtt) REVERT: a 171 MET cc_start: 0.3296 (mmm) cc_final: 0.3064 (mmm) REVERT: a 206 MET cc_start: 0.6098 (mmm) cc_final: 0.5111 (tmm) REVERT: A 148 LEU cc_start: 0.5355 (tp) cc_final: 0.5148 (tp) REVERT: A 498 ASN cc_start: 0.5817 (m-40) cc_final: 0.4773 (t0) REVERT: b 35 ILE cc_start: 0.8806 (mm) cc_final: 0.8524 (tp) REVERT: b 275 MET cc_start: 0.3139 (mmt) cc_final: 0.2740 (mmt) REVERT: b 479 ASP cc_start: 0.5204 (t0) cc_final: 0.4612 (t0) REVERT: B 87 MET cc_start: 0.5628 (mtp) cc_final: 0.5269 (mtm) REVERT: B 112 GLU cc_start: 0.6958 (tp30) cc_final: 0.6603 (tp30) REVERT: B 119 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8310 (tptp) REVERT: B 402 LYS cc_start: 0.8625 (tttt) cc_final: 0.8236 (mptt) REVERT: B 436 MET cc_start: 0.6007 (mtt) cc_final: 0.5238 (mmm) REVERT: B 505 LEU cc_start: 0.8480 (mt) cc_final: 0.8193 (pp) REVERT: D 141 LEU cc_start: 0.7192 (pp) cc_final: 0.6805 (tt) REVERT: D 364 GLU cc_start: 0.3959 (mt-10) cc_final: 0.2777 (pp20) REVERT: D 458 MET cc_start: 0.8167 (mpp) cc_final: 0.7693 (mpp) REVERT: d 121 THR cc_start: 0.9355 (p) cc_final: 0.9148 (p) REVERT: d 128 ILE cc_start: 0.8312 (mp) cc_final: 0.8048 (mm) REVERT: d 129 HIS cc_start: 0.7101 (t-90) cc_final: 0.6653 (t-90) REVERT: d 192 MET cc_start: 0.5576 (mmp) cc_final: 0.4921 (tmm) REVERT: d 214 LEU cc_start: 0.6110 (pt) cc_final: 0.5906 (pt) REVERT: d 282 TYR cc_start: 0.2685 (t80) cc_final: 0.1058 (m-80) REVERT: d 434 LEU cc_start: 0.7050 (tp) cc_final: 0.6715 (tp) REVERT: E 27 MET cc_start: 0.3052 (mtm) cc_final: 0.2651 (mtm) REVERT: E 140 ARG cc_start: 0.7872 (mmp80) cc_final: 0.7651 (mmp80) REVERT: E 147 ASP cc_start: 0.8295 (m-30) cc_final: 0.7933 (m-30) REVERT: E 207 ILE cc_start: 0.3130 (mt) cc_final: 0.2481 (pt) REVERT: E 240 LYS cc_start: 0.5103 (ptpp) cc_final: 0.4812 (ptpp) REVERT: E 286 MET cc_start: 0.5098 (mmt) cc_final: 0.4831 (mmt) REVERT: E 369 MET cc_start: 0.2989 (mtp) cc_final: 0.2167 (mtm) REVERT: E 446 MET cc_start: 0.7404 (mmt) cc_final: 0.6466 (mmt) REVERT: E 491 CYS cc_start: 0.7483 (p) cc_final: 0.7145 (p) REVERT: E 521 MET cc_start: 0.5814 (ttt) cc_final: 0.5447 (ttp) REVERT: e 30 GLU cc_start: 0.7649 (mp0) cc_final: 0.5933 (pt0) REVERT: e 46 MET cc_start: 0.8181 (mmp) cc_final: 0.7081 (mmt) REVERT: e 63 ASP cc_start: 0.5870 (p0) cc_final: 0.5661 (p0) REVERT: e 76 LEU cc_start: 0.7929 (mt) cc_final: 0.7671 (mt) REVERT: e 345 GLU cc_start: 0.4596 (mm-30) cc_final: 0.3979 (pt0) REVERT: e 369 MET cc_start: -0.2495 (mtp) cc_final: -0.4311 (ptp) REVERT: e 513 GLN cc_start: 0.6629 (mm-40) cc_final: 0.6082 (mm-40) REVERT: g 112 PHE cc_start: 0.4616 (m-80) cc_final: 0.3741 (m-80) REVERT: g 237 ARG cc_start: 0.7680 (ttt90) cc_final: 0.7070 (ttm-80) REVERT: g 517 LEU cc_start: 0.7081 (mt) cc_final: 0.6788 (mt) REVERT: h 111 TYR cc_start: 0.5643 (m-10) cc_final: 0.5202 (m-80) REVERT: h 160 MET cc_start: 0.5853 (ppp) cc_final: 0.5518 (ppp) REVERT: h 217 LYS cc_start: 0.4460 (tttt) cc_final: 0.3948 (mttp) REVERT: h 448 GLN cc_start: 0.5532 (mm-40) cc_final: 0.4960 (mm-40) REVERT: h 460 ILE cc_start: 0.7537 (mt) cc_final: 0.7321 (mt) REVERT: H 100 LEU cc_start: 0.7032 (mt) cc_final: 0.6675 (mt) REVERT: H 216 PHE cc_start: 0.3400 (p90) cc_final: 0.3178 (p90) REVERT: H 318 ASP cc_start: 0.4142 (m-30) cc_final: 0.3528 (t70) REVERT: H 358 TYR cc_start: 0.4736 (m-80) cc_final: 0.4362 (m-80) REVERT: H 361 PHE cc_start: -0.2066 (m-80) cc_final: -0.2442 (m-10) REVERT: H 370 CYS cc_start: 0.4113 (p) cc_final: 0.3834 (p) REVERT: H 480 ASN cc_start: 0.7858 (m-40) cc_final: 0.7559 (m-40) REVERT: Q 153 ASN cc_start: 0.5573 (t0) cc_final: 0.5321 (t0) REVERT: Q 161 SER cc_start: 0.7790 (m) cc_final: 0.7164 (p) REVERT: Q 238 LYS cc_start: 0.6625 (mmmt) cc_final: 0.6353 (tttm) REVERT: Q 351 TYR cc_start: 0.3855 (p90) cc_final: 0.3325 (p90) REVERT: Q 519 LEU cc_start: 0.8047 (mm) cc_final: 0.7580 (mt) REVERT: q 62 LYS cc_start: 0.7825 (mmtt) cc_final: 0.7330 (tptm) REVERT: q 114 LEU cc_start: 0.8127 (mm) cc_final: 0.7918 (mm) REVERT: q 179 LEU cc_start: 0.8773 (mt) cc_final: 0.7963 (mt) REVERT: q 315 LEU cc_start: 0.6872 (mt) cc_final: 0.6507 (tp) REVERT: q 320 ASP cc_start: 0.7768 (m-30) cc_final: 0.7435 (m-30) REVERT: q 438 ILE cc_start: 0.6599 (mm) cc_final: 0.6385 (mm) REVERT: q 454 GLU cc_start: 0.6462 (mm-30) cc_final: 0.5826 (mm-30) REVERT: Z 90 ASP cc_start: 0.3920 (t0) cc_final: 0.3537 (t0) REVERT: Z 385 THR cc_start: 0.7224 (m) cc_final: 0.6853 (m) REVERT: z 73 THR cc_start: 0.7612 (m) cc_final: 0.7358 (m) REVERT: z 101 GLU cc_start: 0.6044 (tp30) cc_final: 0.5573 (tp30) REVERT: z 154 THR cc_start: 0.7584 (m) cc_final: 0.7217 (p) outliers start: 1 outliers final: 0 residues processed: 1130 average time/residue: 0.5353 time to fit residues: 1043.2159 Evaluate side-chains 898 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 898 time to evaluate : 4.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 708 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 418 optimal weight: 0.0670 chunk 536 optimal weight: 8.9990 chunk 415 optimal weight: 10.0000 chunk 618 optimal weight: 0.9990 chunk 410 optimal weight: 0.5980 chunk 731 optimal weight: 9.9990 chunk 457 optimal weight: 9.9990 chunk 446 optimal weight: 0.0060 chunk 337 optimal weight: 4.9990 overall best weight: 0.9338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 103 ASN A 492 ASN ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN B 122 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 HIS d 347 HIS ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS ** g 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 GLN G 442 GLN h 301 GLN H 134 ASN H 241 ASN ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN q 93 GLN ** q 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 523 GLN Z 105 GLN ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 105 GLN z 115 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5384 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 59216 Z= 0.166 Angle : 0.573 12.169 79948 Z= 0.286 Chirality : 0.043 0.227 9610 Planarity : 0.004 0.078 10225 Dihedral : 4.644 72.565 8179 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.09), residues: 7598 helix: 0.40 (0.08), residues: 3960 sheet: -1.32 (0.19), residues: 720 loop : -1.30 (0.11), residues: 2918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 474 HIS 0.007 0.001 HIS d 347 PHE 0.029 0.001 PHE q 399 TYR 0.028 0.001 TYR H 275 ARG 0.009 0.000 ARG h 398 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1144 time to evaluate : 4.982 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 73 LYS cc_start: 0.7234 (mmtt) cc_final: 0.6896 (mmtt) REVERT: a 117 VAL cc_start: 0.7563 (t) cc_final: 0.7328 (t) REVERT: a 206 MET cc_start: 0.6238 (mmm) cc_final: 0.5088 (tmm) REVERT: A 148 LEU cc_start: 0.5372 (tp) cc_final: 0.5100 (tp) REVERT: A 498 ASN cc_start: 0.5420 (m-40) cc_final: 0.4862 (t0) REVERT: b 275 MET cc_start: 0.3744 (mmt) cc_final: 0.3535 (mmt) REVERT: b 314 HIS cc_start: 0.2707 (t70) cc_final: 0.2376 (p-80) REVERT: b 479 ASP cc_start: 0.5201 (t0) cc_final: 0.4197 (t0) REVERT: B 87 MET cc_start: 0.5766 (mtp) cc_final: 0.5515 (mtm) REVERT: B 112 GLU cc_start: 0.7035 (tp30) cc_final: 0.6780 (tp30) REVERT: B 119 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8368 (tptp) REVERT: B 402 LYS cc_start: 0.8638 (tttt) cc_final: 0.8187 (mptt) REVERT: B 436 MET cc_start: 0.5855 (mtt) cc_final: 0.5293 (mmm) REVERT: B 488 MET cc_start: 0.6455 (mmm) cc_final: 0.5705 (mmm) REVERT: B 505 LEU cc_start: 0.8493 (mt) cc_final: 0.8253 (pp) REVERT: D 37 ASN cc_start: 0.6754 (t0) cc_final: 0.6337 (t0) REVERT: D 93 GLU cc_start: 0.6739 (mp0) cc_final: 0.6522 (pm20) REVERT: D 141 LEU cc_start: 0.7194 (pp) cc_final: 0.6733 (tt) REVERT: D 364 GLU cc_start: 0.3947 (mt-10) cc_final: 0.2750 (pp20) REVERT: D 458 MET cc_start: 0.8048 (mpp) cc_final: 0.7740 (mpp) REVERT: d 96 LYS cc_start: 0.7248 (mmmt) cc_final: 0.6734 (mmmt) REVERT: d 129 HIS cc_start: 0.6912 (t-90) cc_final: 0.6543 (t-90) REVERT: d 192 MET cc_start: 0.5471 (mmp) cc_final: 0.4863 (tmm) REVERT: d 211 VAL cc_start: 0.3791 (t) cc_final: 0.3473 (m) REVERT: d 214 LEU cc_start: 0.6287 (pt) cc_final: 0.5446 (tt) REVERT: d 282 TYR cc_start: 0.2663 (t80) cc_final: 0.1066 (m-80) REVERT: d 396 LEU cc_start: 0.5470 (tp) cc_final: 0.5169 (tp) REVERT: d 434 LEU cc_start: 0.6998 (tp) cc_final: 0.6646 (tp) REVERT: E 27 MET cc_start: 0.3015 (mtm) cc_final: 0.2677 (mtm) REVERT: E 89 MET cc_start: 0.6886 (mmt) cc_final: 0.6618 (mmt) REVERT: E 147 ASP cc_start: 0.8406 (m-30) cc_final: 0.7860 (m-30) REVERT: E 207 ILE cc_start: 0.3096 (mt) cc_final: 0.2487 (pt) REVERT: E 240 LYS cc_start: 0.5426 (ptpp) cc_final: 0.5112 (ptpp) REVERT: E 286 MET cc_start: 0.5098 (mmt) cc_final: 0.4797 (mmt) REVERT: E 369 MET cc_start: 0.2626 (mtp) cc_final: 0.1877 (mtm) REVERT: E 446 MET cc_start: 0.7304 (mmt) cc_final: 0.6402 (mmt) REVERT: E 491 CYS cc_start: 0.7418 (p) cc_final: 0.7026 (p) REVERT: e 30 GLU cc_start: 0.7672 (mp0) cc_final: 0.5931 (pt0) REVERT: e 46 MET cc_start: 0.8102 (mmp) cc_final: 0.6958 (mmt) REVERT: e 58 MET cc_start: 0.7401 (ppp) cc_final: 0.7063 (ppp) REVERT: e 63 ASP cc_start: 0.5804 (p0) cc_final: 0.5591 (p0) REVERT: e 345 GLU cc_start: 0.4677 (mm-30) cc_final: 0.3995 (pt0) REVERT: e 369 MET cc_start: -0.2586 (mtp) cc_final: -0.4358 (ptp) REVERT: g 112 PHE cc_start: 0.4423 (m-80) cc_final: 0.3503 (m-80) REVERT: g 151 MET cc_start: 0.6222 (tmm) cc_final: 0.5226 (tpt) REVERT: g 237 ARG cc_start: 0.7649 (ttt90) cc_final: 0.7065 (ttm-80) REVERT: g 517 LEU cc_start: 0.7047 (mt) cc_final: 0.6747 (mt) REVERT: h 111 TYR cc_start: 0.5463 (m-10) cc_final: 0.5190 (m-80) REVERT: h 160 MET cc_start: 0.5769 (ppp) cc_final: 0.5416 (ppp) REVERT: h 217 LYS cc_start: 0.4586 (tttt) cc_final: 0.4011 (mttp) REVERT: h 382 MET cc_start: -0.1257 (mtp) cc_final: -0.1827 (mmm) REVERT: h 448 GLN cc_start: 0.5471 (mm-40) cc_final: 0.5265 (mm-40) REVERT: h 460 ILE cc_start: 0.7496 (mt) cc_final: 0.7249 (mt) REVERT: h 520 ILE cc_start: 0.8364 (mm) cc_final: 0.8053 (mm) REVERT: H 100 LEU cc_start: 0.6994 (mt) cc_final: 0.6637 (mt) REVERT: H 216 PHE cc_start: 0.3377 (p90) cc_final: 0.3087 (p90) REVERT: H 318 ASP cc_start: 0.4150 (m-30) cc_final: 0.3511 (t0) REVERT: H 348 PHE cc_start: 0.0069 (t80) cc_final: -0.0166 (t80) REVERT: H 358 TYR cc_start: 0.4834 (m-80) cc_final: 0.4488 (m-80) REVERT: H 361 PHE cc_start: -0.2075 (m-80) cc_final: -0.2469 (m-10) REVERT: H 370 CYS cc_start: 0.4016 (p) cc_final: 0.3551 (p) REVERT: H 480 ASN cc_start: 0.7865 (m-40) cc_final: 0.7575 (m-40) REVERT: Q 161 SER cc_start: 0.7718 (m) cc_final: 0.6947 (p) REVERT: Q 230 ASP cc_start: 0.4840 (t70) cc_final: 0.4354 (p0) REVERT: Q 351 TYR cc_start: 0.3673 (p90) cc_final: 0.3163 (p90) REVERT: Q 419 LEU cc_start: 0.7376 (tp) cc_final: 0.7133 (tp) REVERT: Q 519 LEU cc_start: 0.8031 (mm) cc_final: 0.7514 (mt) REVERT: q 62 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7339 (tptm) REVERT: q 114 LEU cc_start: 0.8003 (mm) cc_final: 0.7767 (mm) REVERT: q 179 LEU cc_start: 0.8795 (mt) cc_final: 0.8520 (mt) REVERT: q 315 LEU cc_start: 0.6910 (mt) cc_final: 0.6511 (tp) REVERT: q 320 ASP cc_start: 0.7805 (m-30) cc_final: 0.7402 (m-30) REVERT: q 438 ILE cc_start: 0.6551 (mm) cc_final: 0.6320 (mm) REVERT: q 454 GLU cc_start: 0.6377 (mm-30) cc_final: 0.5689 (mm-30) REVERT: Z 90 ASP cc_start: 0.4255 (t0) cc_final: 0.3877 (t0) REVERT: Z 385 THR cc_start: 0.6939 (m) cc_final: 0.6571 (m) REVERT: z 101 GLU cc_start: 0.6013 (tp30) cc_final: 0.5409 (tp30) REVERT: z 102 LEU cc_start: 0.8030 (mt) cc_final: 0.7748 (mp) REVERT: z 154 THR cc_start: 0.7586 (m) cc_final: 0.7140 (p) REVERT: z 196 MET cc_start: 0.5511 (mmm) cc_final: 0.5248 (mmm) REVERT: z 208 ARG cc_start: 0.5272 (mmp80) cc_final: 0.5017 (mmp80) outliers start: 0 outliers final: 0 residues processed: 1144 average time/residue: 0.5510 time to fit residues: 1088.7294 Evaluate side-chains 916 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 916 time to evaluate : 4.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 452 optimal weight: 10.0000 chunk 292 optimal weight: 0.0980 chunk 436 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 141 optimal weight: 0.4980 chunk 465 optimal weight: 8.9990 chunk 498 optimal weight: 3.9990 chunk 361 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 575 optimal weight: 0.8980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 103 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN H 241 ASN ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 175 ASN Q 365 HIS q 93 GLN q 185 GLN q 523 GLN ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 115 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5448 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 59216 Z= 0.208 Angle : 0.615 12.933 79948 Z= 0.308 Chirality : 0.044 0.188 9610 Planarity : 0.004 0.079 10225 Dihedral : 4.796 69.102 8179 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.02 % Allowed : 1.02 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.09), residues: 7598 helix: 0.34 (0.08), residues: 3947 sheet: -1.36 (0.19), residues: 710 loop : -1.31 (0.11), residues: 2941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 474 HIS 0.010 0.001 HIS d 347 PHE 0.027 0.002 PHE q 103 TYR 0.046 0.002 TYR h 423 ARG 0.013 0.001 ARG z 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1110 time to evaluate : 5.008 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 ASP cc_start: 0.7151 (m-30) cc_final: 0.6929 (m-30) REVERT: a 73 LYS cc_start: 0.7324 (mmtt) cc_final: 0.6901 (mmtt) REVERT: a 117 VAL cc_start: 0.7643 (t) cc_final: 0.7438 (t) REVERT: a 171 MET cc_start: 0.3177 (mmm) cc_final: 0.1598 (tmm) REVERT: a 345 LEU cc_start: 0.5257 (mp) cc_final: 0.4945 (tt) REVERT: a 384 MET cc_start: -0.0153 (ptm) cc_final: -0.1163 (ptm) REVERT: A 148 LEU cc_start: 0.5104 (tp) cc_final: 0.4840 (tp) REVERT: A 225 MET cc_start: 0.0604 (mmp) cc_final: 0.0103 (mtm) REVERT: A 306 MET cc_start: 0.2982 (tpt) cc_final: 0.0935 (mmt) REVERT: b 275 MET cc_start: 0.3755 (mmt) cc_final: 0.3431 (mmt) REVERT: b 388 ARG cc_start: 0.6744 (ptt180) cc_final: 0.5767 (ptm-80) REVERT: b 449 ILE cc_start: 0.7999 (mt) cc_final: 0.7634 (mt) REVERT: B 87 MET cc_start: 0.5670 (mtp) cc_final: 0.5187 (mtm) REVERT: B 112 GLU cc_start: 0.6846 (tp30) cc_final: 0.6554 (tp30) REVERT: B 119 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8405 (pttm) REVERT: B 160 MET cc_start: 0.7225 (ppp) cc_final: 0.6730 (ppp) REVERT: B 402 LYS cc_start: 0.8692 (tttt) cc_final: 0.8251 (mptt) REVERT: B 436 MET cc_start: 0.6008 (mtt) cc_final: 0.5456 (mmm) REVERT: B 505 LEU cc_start: 0.8542 (mt) cc_final: 0.8263 (pp) REVERT: D 59 LYS cc_start: 0.7254 (mmtp) cc_final: 0.7034 (mmtp) REVERT: D 79 LYS cc_start: 0.6610 (ptpt) cc_final: 0.6233 (ptpp) REVERT: D 141 LEU cc_start: 0.7217 (pp) cc_final: 0.6789 (tt) REVERT: D 364 GLU cc_start: 0.3756 (mt-10) cc_final: 0.2344 (pp20) REVERT: D 391 ARG cc_start: 0.3160 (mtp180) cc_final: 0.2103 (mmm160) REVERT: D 458 MET cc_start: 0.8130 (mpp) cc_final: 0.7732 (mpp) REVERT: d 95 SER cc_start: 0.8046 (m) cc_final: 0.7830 (p) REVERT: d 129 HIS cc_start: 0.7145 (t-90) cc_final: 0.6741 (t-90) REVERT: d 192 MET cc_start: 0.5493 (mmp) cc_final: 0.4955 (tmm) REVERT: d 214 LEU cc_start: 0.6334 (pt) cc_final: 0.6088 (pt) REVERT: d 282 TYR cc_start: 0.2693 (t80) cc_final: 0.1073 (m-80) REVERT: d 396 LEU cc_start: 0.5519 (tp) cc_final: 0.5211 (tp) REVERT: d 434 LEU cc_start: 0.7048 (tp) cc_final: 0.6747 (tp) REVERT: E 27 MET cc_start: 0.3067 (mtm) cc_final: 0.2710 (mtm) REVERT: E 46 MET cc_start: 0.7381 (mmm) cc_final: 0.7139 (mmm) REVERT: E 147 ASP cc_start: 0.8335 (m-30) cc_final: 0.7818 (m-30) REVERT: E 204 PHE cc_start: 0.5804 (t80) cc_final: 0.5533 (t80) REVERT: E 207 ILE cc_start: 0.3233 (mt) cc_final: 0.2746 (pt) REVERT: E 237 MET cc_start: 0.1480 (mmt) cc_final: -0.0184 (mtt) REVERT: E 240 LYS cc_start: 0.5198 (ptpp) cc_final: 0.4890 (ptpp) REVERT: E 286 MET cc_start: 0.5119 (mmt) cc_final: 0.4814 (mmt) REVERT: E 369 MET cc_start: 0.2476 (mtp) cc_final: 0.1742 (mtm) REVERT: E 446 MET cc_start: 0.7709 (mmt) cc_final: 0.6600 (mmt) REVERT: e 30 GLU cc_start: 0.7652 (mp0) cc_final: 0.5922 (pt0) REVERT: e 46 MET cc_start: 0.8217 (mmp) cc_final: 0.7003 (mmp) REVERT: e 58 MET cc_start: 0.7366 (ppp) cc_final: 0.7083 (ppp) REVERT: e 345 GLU cc_start: 0.4699 (mm-30) cc_final: 0.3997 (pt0) REVERT: e 369 MET cc_start: -0.2546 (mtp) cc_final: -0.4123 (ptp) REVERT: e 472 MET cc_start: 0.6969 (tpp) cc_final: 0.6712 (tpp) REVERT: g 112 PHE cc_start: 0.4425 (m-80) cc_final: 0.3560 (m-80) REVERT: g 237 ARG cc_start: 0.7680 (ttt90) cc_final: 0.7057 (ttm-80) REVERT: h 160 MET cc_start: 0.5892 (ppp) cc_final: 0.5538 (ppp) REVERT: h 217 LYS cc_start: 0.4607 (tttt) cc_final: 0.4107 (mttp) REVERT: h 382 MET cc_start: -0.1534 (mtp) cc_final: -0.2133 (mmm) REVERT: h 448 GLN cc_start: 0.5900 (mm-40) cc_final: 0.5671 (mm-40) REVERT: H 100 LEU cc_start: 0.6941 (mt) cc_final: 0.6574 (mt) REVERT: H 211 VAL cc_start: 0.4522 (t) cc_final: 0.4311 (t) REVERT: H 318 ASP cc_start: 0.4102 (m-30) cc_final: 0.3488 (t0) REVERT: H 358 TYR cc_start: 0.4814 (m-80) cc_final: 0.4474 (m-80) REVERT: H 361 PHE cc_start: -0.1888 (m-80) cc_final: -0.2225 (m-10) REVERT: H 370 CYS cc_start: 0.3842 (p) cc_final: 0.3490 (p) REVERT: H 423 TYR cc_start: 0.6836 (t80) cc_final: 0.6611 (t80) REVERT: H 480 ASN cc_start: 0.7851 (m-40) cc_final: 0.7343 (m-40) REVERT: Q 73 LEU cc_start: 0.6907 (mt) cc_final: 0.6523 (mt) REVERT: Q 161 SER cc_start: 0.7834 (m) cc_final: 0.7208 (p) REVERT: Q 351 TYR cc_start: 0.3391 (p90) cc_final: 0.2871 (p90) REVERT: Q 519 LEU cc_start: 0.8200 (mm) cc_final: 0.7657 (mt) REVERT: q 62 LYS cc_start: 0.7816 (mmtt) cc_final: 0.7284 (tptm) REVERT: q 114 LEU cc_start: 0.7892 (mm) cc_final: 0.7634 (mm) REVERT: q 130 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6498 (mm-30) REVERT: q 175 ASN cc_start: 0.7589 (t0) cc_final: 0.7240 (t0) REVERT: q 179 LEU cc_start: 0.8832 (mt) cc_final: 0.8069 (mt) REVERT: q 185 GLN cc_start: 0.6474 (OUTLIER) cc_final: 0.6215 (pp30) REVERT: q 311 MET cc_start: 0.0214 (tpp) cc_final: -0.0175 (mmm) REVERT: q 315 LEU cc_start: 0.6489 (mt) cc_final: 0.6120 (tp) REVERT: q 320 ASP cc_start: 0.8033 (m-30) cc_final: 0.7702 (m-30) REVERT: q 438 ILE cc_start: 0.6608 (mm) cc_final: 0.6386 (mm) REVERT: q 454 GLU cc_start: 0.6434 (mm-30) cc_final: 0.5674 (mm-30) REVERT: Z 90 ASP cc_start: 0.4090 (t0) cc_final: 0.3674 (t0) REVERT: Z 385 THR cc_start: 0.7006 (m) cc_final: 0.6626 (m) REVERT: z 101 GLU cc_start: 0.6163 (tp30) cc_final: 0.5524 (tp30) REVERT: z 102 LEU cc_start: 0.8145 (mt) cc_final: 0.7878 (mp) outliers start: 1 outliers final: 0 residues processed: 1111 average time/residue: 0.5850 time to fit residues: 1127.5030 Evaluate side-chains 896 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 895 time to evaluate : 5.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 665 optimal weight: 9.9990 chunk 700 optimal weight: 9.9990 chunk 639 optimal weight: 0.0670 chunk 681 optimal weight: 0.0970 chunk 410 optimal weight: 0.7980 chunk 296 optimal weight: 0.9990 chunk 535 optimal weight: 9.9990 chunk 209 optimal weight: 7.9990 chunk 616 optimal weight: 1.9990 chunk 644 optimal weight: 6.9990 chunk 679 optimal weight: 3.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 103 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 HIS d 347 HIS E 44 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 406 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN H 241 ASN ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 93 GLN ** q 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 523 GLN Z 105 GLN ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5391 moved from start: 0.5808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 59216 Z= 0.161 Angle : 0.593 12.957 79948 Z= 0.294 Chirality : 0.043 0.188 9610 Planarity : 0.004 0.079 10225 Dihedral : 4.633 59.320 8179 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.10), residues: 7598 helix: 0.49 (0.08), residues: 3940 sheet: -1.29 (0.19), residues: 689 loop : -1.21 (0.11), residues: 2969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 474 HIS 0.007 0.001 HIS d 347 PHE 0.022 0.001 PHE q 103 TYR 0.038 0.001 TYR h 423 ARG 0.008 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1101 time to evaluate : 4.978 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 73 LYS cc_start: 0.7258 (mmtt) cc_final: 0.6908 (mmtt) REVERT: a 112 ILE cc_start: 0.7787 (mp) cc_final: 0.7577 (mp) REVERT: a 171 MET cc_start: 0.4390 (mmt) cc_final: 0.3379 (tmm) REVERT: a 206 MET cc_start: 0.5778 (mmm) cc_final: 0.5364 (tmm) REVERT: a 345 LEU cc_start: 0.5173 (mp) cc_final: 0.4811 (tt) REVERT: a 384 MET cc_start: 0.0633 (ptm) cc_final: -0.0434 (ptm) REVERT: A 148 LEU cc_start: 0.5655 (tp) cc_final: 0.5420 (tp) REVERT: A 225 MET cc_start: 0.0561 (mmp) cc_final: 0.0068 (mtm) REVERT: A 306 MET cc_start: 0.3525 (tpt) cc_final: 0.1473 (mmt) REVERT: b 141 LEU cc_start: 0.7970 (mp) cc_final: 0.7385 (mp) REVERT: b 275 MET cc_start: 0.3973 (mmt) cc_final: 0.3669 (mmt) REVERT: b 388 ARG cc_start: 0.6831 (ptt180) cc_final: 0.5807 (ptm-80) REVERT: b 449 ILE cc_start: 0.8056 (mt) cc_final: 0.7722 (mt) REVERT: b 501 ARG cc_start: 0.7251 (ttp80) cc_final: 0.6492 (ptt90) REVERT: B 402 LYS cc_start: 0.8615 (tttt) cc_final: 0.8176 (mmtm) REVERT: B 505 LEU cc_start: 0.8444 (mt) cc_final: 0.8094 (pp) REVERT: D 36 SER cc_start: 0.8001 (t) cc_final: 0.7550 (p) REVERT: D 104 ASP cc_start: 0.6591 (m-30) cc_final: 0.6344 (m-30) REVERT: D 118 ASP cc_start: 0.6780 (t0) cc_final: 0.6387 (t0) REVERT: D 141 LEU cc_start: 0.7161 (pp) cc_final: 0.6871 (tt) REVERT: D 364 GLU cc_start: 0.3863 (mt-10) cc_final: 0.2564 (pp20) REVERT: d 95 SER cc_start: 0.8148 (m) cc_final: 0.7873 (p) REVERT: d 129 HIS cc_start: 0.7103 (t-90) cc_final: 0.6748 (t-90) REVERT: d 192 MET cc_start: 0.5521 (mmp) cc_final: 0.4909 (tmm) REVERT: d 210 ILE cc_start: 0.3243 (mt) cc_final: 0.2893 (mp) REVERT: d 214 LEU cc_start: 0.6280 (pt) cc_final: 0.6031 (pt) REVERT: d 396 LEU cc_start: 0.5252 (tp) cc_final: 0.4981 (tp) REVERT: d 434 LEU cc_start: 0.6983 (tp) cc_final: 0.6691 (tp) REVERT: E 46 MET cc_start: 0.7399 (mmm) cc_final: 0.7192 (mmm) REVERT: E 147 ASP cc_start: 0.8294 (m-30) cc_final: 0.7701 (m-30) REVERT: E 207 ILE cc_start: 0.3111 (mt) cc_final: 0.2417 (pt) REVERT: E 218 GLU cc_start: 0.5852 (pm20) cc_final: 0.5538 (tp30) REVERT: E 286 MET cc_start: 0.4848 (mmt) cc_final: 0.4557 (mmt) REVERT: E 369 MET cc_start: 0.2617 (mtp) cc_final: 0.1881 (mtm) REVERT: E 446 MET cc_start: 0.7379 (mmt) cc_final: 0.6512 (mmt) REVERT: E 491 CYS cc_start: 0.7193 (p) cc_final: 0.6907 (p) REVERT: e 30 GLU cc_start: 0.7660 (mp0) cc_final: 0.5928 (pt0) REVERT: e 46 MET cc_start: 0.7870 (mmp) cc_final: 0.6709 (mmt) REVERT: e 345 GLU cc_start: 0.4704 (mm-30) cc_final: 0.3993 (pt0) REVERT: e 369 MET cc_start: -0.2503 (mtp) cc_final: -0.4316 (ptp) REVERT: g 46 MET cc_start: 0.8419 (mmm) cc_final: 0.7959 (mmm) REVERT: g 112 PHE cc_start: 0.4301 (m-80) cc_final: 0.3626 (m-80) REVERT: g 237 ARG cc_start: 0.7661 (ttt90) cc_final: 0.7063 (ttm-80) REVERT: g 517 LEU cc_start: 0.7189 (mt) cc_final: 0.6944 (mt) REVERT: G 151 MET cc_start: 0.4013 (ppp) cc_final: 0.3534 (mmp) REVERT: G 440 VAL cc_start: 0.6902 (t) cc_final: 0.6693 (t) REVERT: h 160 MET cc_start: 0.5645 (ppp) cc_final: 0.5391 (ppp) REVERT: h 217 LYS cc_start: 0.4789 (tttt) cc_final: 0.4377 (mmmt) REVERT: h 382 MET cc_start: -0.1093 (mtp) cc_final: -0.1604 (mmm) REVERT: h 448 GLN cc_start: 0.5810 (mm-40) cc_final: 0.5602 (mm-40) REVERT: h 520 ILE cc_start: 0.8359 (mm) cc_final: 0.8088 (mm) REVERT: H 100 LEU cc_start: 0.6800 (mt) cc_final: 0.6439 (mt) REVERT: H 358 TYR cc_start: 0.4742 (m-80) cc_final: 0.4382 (m-80) REVERT: H 361 PHE cc_start: -0.1883 (m-80) cc_final: -0.2215 (m-10) REVERT: H 370 CYS cc_start: 0.3791 (p) cc_final: 0.3560 (p) REVERT: H 480 ASN cc_start: 0.7869 (m-40) cc_final: 0.7369 (m-40) REVERT: Q 73 LEU cc_start: 0.6837 (mt) cc_final: 0.6384 (mt) REVERT: Q 161 SER cc_start: 0.7644 (m) cc_final: 0.6951 (p) REVERT: Q 238 LYS cc_start: 0.6215 (tppt) cc_final: 0.5809 (tmtt) REVERT: Q 351 TYR cc_start: 0.3522 (p90) cc_final: 0.2884 (p90) REVERT: Q 419 LEU cc_start: 0.7350 (tp) cc_final: 0.7130 (tp) REVERT: q 43 THR cc_start: 0.7469 (m) cc_final: 0.7258 (m) REVERT: q 62 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7265 (tptm) REVERT: q 114 LEU cc_start: 0.7758 (mm) cc_final: 0.7515 (mm) REVERT: q 130 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6453 (mm-30) REVERT: q 175 ASN cc_start: 0.7551 (t0) cc_final: 0.7238 (t0) REVERT: q 179 LEU cc_start: 0.8759 (mt) cc_final: 0.8050 (mt) REVERT: q 311 MET cc_start: -0.0073 (tpp) cc_final: -0.0362 (mmm) REVERT: q 315 LEU cc_start: 0.6939 (mt) cc_final: 0.6663 (tp) REVERT: q 320 ASP cc_start: 0.7803 (m-30) cc_final: 0.7406 (m-30) REVERT: q 438 ILE cc_start: 0.6483 (mm) cc_final: 0.6237 (mm) REVERT: q 454 GLU cc_start: 0.6381 (mm-30) cc_final: 0.5571 (mm-30) REVERT: Z 43 THR cc_start: 0.4092 (p) cc_final: 0.3709 (p) REVERT: Z 90 ASP cc_start: 0.4390 (t0) cc_final: 0.3882 (t0) REVERT: Z 143 MET cc_start: 0.5562 (ppp) cc_final: 0.5348 (tmm) REVERT: Z 385 THR cc_start: 0.6702 (m) cc_final: 0.6384 (m) REVERT: z 101 GLU cc_start: 0.6021 (tp30) cc_final: 0.5325 (tp30) REVERT: z 154 THR cc_start: 0.7521 (m) cc_final: 0.7109 (p) REVERT: z 208 ARG cc_start: 0.5334 (mmp80) cc_final: 0.4999 (mmp80) REVERT: z 221 MET cc_start: 0.1471 (ppp) cc_final: 0.1185 (ppp) outliers start: 0 outliers final: 0 residues processed: 1101 average time/residue: 0.5345 time to fit residues: 1018.2254 Evaluate side-chains 891 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 891 time to evaluate : 4.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 447 optimal weight: 30.0000 chunk 720 optimal weight: 2.9990 chunk 439 optimal weight: 4.9990 chunk 341 optimal weight: 0.0570 chunk 501 optimal weight: 20.0000 chunk 756 optimal weight: 0.9990 chunk 695 optimal weight: 7.9990 chunk 602 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 465 optimal weight: 0.4980 chunk 369 optimal weight: 0.9990 overall best weight: 0.9104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 103 ASN a 110 GLN a 133 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 347 HIS E 44 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 454 ASN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN H 241 ASN ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 ASN Q 175 ASN q 93 GLN q 172 GLN ** q 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 523 GLN ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 105 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5389 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 59216 Z= 0.166 Angle : 0.610 13.522 79948 Z= 0.301 Chirality : 0.043 0.204 9610 Planarity : 0.004 0.079 10225 Dihedral : 4.686 68.546 8179 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.10), residues: 7598 helix: 0.54 (0.08), residues: 3932 sheet: -1.24 (0.19), residues: 708 loop : -1.16 (0.11), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 271 HIS 0.008 0.001 HIS H 117 PHE 0.023 0.001 PHE q 103 TYR 0.034 0.001 TYR h 423 ARG 0.009 0.000 ARG A 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1083 time to evaluate : 4.983 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 73 LYS cc_start: 0.7112 (mmtt) cc_final: 0.6899 (mmtt) REVERT: a 156 MET cc_start: 0.2490 (ppp) cc_final: 0.2190 (ppp) REVERT: a 171 MET cc_start: 0.4370 (mmt) cc_final: 0.3441 (tmm) REVERT: a 206 MET cc_start: 0.5798 (mmm) cc_final: 0.5365 (tmm) REVERT: a 345 LEU cc_start: 0.5158 (mp) cc_final: 0.4803 (tt) REVERT: a 384 MET cc_start: -0.0574 (ptm) cc_final: -0.1312 (ptm) REVERT: A 148 LEU cc_start: 0.5543 (tp) cc_final: 0.5298 (tp) REVERT: A 225 MET cc_start: 0.0514 (mmp) cc_final: 0.0115 (mtp) REVERT: A 306 MET cc_start: 0.3085 (tpt) cc_final: 0.1276 (mmt) REVERT: b 111 ARG cc_start: 0.8584 (mtp85) cc_final: 0.8296 (ttm-80) REVERT: b 275 MET cc_start: 0.3964 (mmt) cc_final: 0.3647 (mmt) REVERT: b 314 HIS cc_start: 0.2728 (t70) cc_final: 0.2481 (p90) REVERT: b 388 ARG cc_start: 0.6854 (ptt180) cc_final: 0.5802 (ptm-80) REVERT: b 449 ILE cc_start: 0.7882 (mt) cc_final: 0.7556 (mt) REVERT: b 501 ARG cc_start: 0.7257 (ttp80) cc_final: 0.6486 (ptt90) REVERT: B 112 GLU cc_start: 0.6939 (tp30) cc_final: 0.6703 (tp30) REVERT: B 402 LYS cc_start: 0.8594 (tttt) cc_final: 0.8160 (mptt) REVERT: B 505 LEU cc_start: 0.8618 (mt) cc_final: 0.8324 (pp) REVERT: D 93 GLU cc_start: 0.6916 (mp0) cc_final: 0.6573 (pm20) REVERT: D 104 ASP cc_start: 0.6606 (m-30) cc_final: 0.6309 (m-30) REVERT: D 118 ASP cc_start: 0.6702 (t0) cc_final: 0.6306 (t0) REVERT: D 138 GLN cc_start: 0.4281 (pp30) cc_final: 0.4051 (pp30) REVERT: D 141 LEU cc_start: 0.7151 (pp) cc_final: 0.6855 (tt) REVERT: D 364 GLU cc_start: 0.3868 (mt-10) cc_final: 0.2563 (pp20) REVERT: d 95 SER cc_start: 0.8128 (m) cc_final: 0.7888 (p) REVERT: d 129 HIS cc_start: 0.7090 (t-90) cc_final: 0.6728 (t-90) REVERT: d 192 MET cc_start: 0.5516 (mmp) cc_final: 0.4913 (tmm) REVERT: d 210 ILE cc_start: 0.3201 (mt) cc_final: 0.2888 (mp) REVERT: d 214 LEU cc_start: 0.6225 (pt) cc_final: 0.5975 (pt) REVERT: d 396 LEU cc_start: 0.5239 (tp) cc_final: 0.4908 (tp) REVERT: d 434 LEU cc_start: 0.6953 (tp) cc_final: 0.6678 (tp) REVERT: E 46 MET cc_start: 0.7288 (mmm) cc_final: 0.7065 (mmm) REVERT: E 147 ASP cc_start: 0.8296 (m-30) cc_final: 0.7718 (m-30) REVERT: E 185 GLU cc_start: 0.5615 (tt0) cc_final: 0.4709 (pt0) REVERT: E 207 ILE cc_start: 0.3207 (mt) cc_final: 0.2473 (pt) REVERT: E 218 GLU cc_start: 0.5823 (pm20) cc_final: 0.5439 (tp30) REVERT: E 286 MET cc_start: 0.4845 (mmt) cc_final: 0.4571 (mmt) REVERT: E 369 MET cc_start: 0.2490 (mtp) cc_final: 0.1906 (mtm) REVERT: E 491 CYS cc_start: 0.7155 (p) cc_final: 0.6883 (p) REVERT: E 521 MET cc_start: 0.4139 (mtp) cc_final: 0.3880 (mtm) REVERT: e 30 GLU cc_start: 0.7676 (mp0) cc_final: 0.5956 (pt0) REVERT: e 46 MET cc_start: 0.7919 (mmp) cc_final: 0.6694 (mmt) REVERT: e 345 GLU cc_start: 0.4737 (mm-30) cc_final: 0.4005 (pt0) REVERT: e 369 MET cc_start: -0.2501 (mtp) cc_final: -0.4335 (ptp) REVERT: e 472 MET cc_start: 0.7147 (tpp) cc_final: 0.6722 (tpp) REVERT: g 112 PHE cc_start: 0.4577 (m-80) cc_final: 0.3853 (m-80) REVERT: g 192 GLU cc_start: 0.6654 (pp20) cc_final: 0.6055 (pp20) REVERT: g 237 ARG cc_start: 0.7663 (ttt90) cc_final: 0.7065 (ttm-80) REVERT: g 517 LEU cc_start: 0.7202 (mt) cc_final: 0.6881 (mt) REVERT: G 180 VAL cc_start: 0.7213 (t) cc_final: 0.6985 (t) REVERT: G 440 VAL cc_start: 0.6861 (t) cc_final: 0.6647 (t) REVERT: h 160 MET cc_start: 0.5680 (ppp) cc_final: 0.5365 (ppp) REVERT: h 217 LYS cc_start: 0.4835 (tttt) cc_final: 0.4407 (mmmt) REVERT: h 382 MET cc_start: -0.0978 (mtp) cc_final: -0.1505 (mmm) REVERT: h 460 ILE cc_start: 0.7550 (mt) cc_final: 0.7327 (mt) REVERT: h 520 ILE cc_start: 0.8316 (mm) cc_final: 0.8087 (mm) REVERT: H 100 LEU cc_start: 0.6781 (mt) cc_final: 0.6439 (mt) REVERT: H 358 TYR cc_start: 0.4766 (m-80) cc_final: 0.4405 (m-80) REVERT: H 370 CYS cc_start: 0.3266 (p) cc_final: 0.2860 (p) REVERT: H 422 ASP cc_start: 0.6435 (m-30) cc_final: 0.6111 (p0) REVERT: H 480 ASN cc_start: 0.7849 (m-40) cc_final: 0.7321 (m-40) REVERT: Q 73 LEU cc_start: 0.6865 (mt) cc_final: 0.6454 (mt) REVERT: Q 161 SER cc_start: 0.7906 (m) cc_final: 0.7144 (p) REVERT: Q 238 LYS cc_start: 0.6123 (tppt) cc_final: 0.5708 (tmtt) REVERT: Q 311 MET cc_start: -0.0314 (ttp) cc_final: -0.0585 (ttp) REVERT: Q 351 TYR cc_start: 0.3248 (p90) cc_final: 0.2853 (p90) REVERT: q 52 MET cc_start: 0.6369 (mmt) cc_final: 0.5926 (mmt) REVERT: q 62 LYS cc_start: 0.7929 (mmtt) cc_final: 0.7341 (tptm) REVERT: q 114 LEU cc_start: 0.7826 (mm) cc_final: 0.7571 (mm) REVERT: q 130 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6482 (mm-30) REVERT: q 171 LYS cc_start: 0.4671 (mmtt) cc_final: 0.4278 (mptt) REVERT: q 175 ASN cc_start: 0.7505 (t0) cc_final: 0.7157 (t0) REVERT: q 179 LEU cc_start: 0.8738 (mt) cc_final: 0.8012 (mt) REVERT: q 311 MET cc_start: -0.0243 (tpp) cc_final: -0.0462 (mmm) REVERT: q 315 LEU cc_start: 0.6935 (mt) cc_final: 0.6664 (tp) REVERT: q 320 ASP cc_start: 0.7865 (m-30) cc_final: 0.7505 (m-30) REVERT: q 438 ILE cc_start: 0.6474 (mm) cc_final: 0.6263 (mm) REVERT: q 454 GLU cc_start: 0.6353 (mm-30) cc_final: 0.5644 (mm-30) REVERT: Z 43 THR cc_start: 0.4007 (p) cc_final: 0.3571 (p) REVERT: Z 90 ASP cc_start: 0.4481 (t0) cc_final: 0.3988 (t0) REVERT: Z 385 THR cc_start: 0.6979 (m) cc_final: 0.6675 (m) REVERT: z 101 GLU cc_start: 0.5922 (tp30) cc_final: 0.5322 (tp30) REVERT: z 154 THR cc_start: 0.7560 (m) cc_final: 0.7142 (p) outliers start: 0 outliers final: 0 residues processed: 1083 average time/residue: 0.5496 time to fit residues: 1033.8023 Evaluate side-chains 887 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 887 time to evaluate : 4.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 478 optimal weight: 0.8980 chunk 641 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 555 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 603 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 619 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 111 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 347 HIS E 44 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 137 GLN g 115 GLN ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 420 HIS ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 241 ASN ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 93 GLN q 172 GLN ** q 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 523 GLN ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 115 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.181789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.159661 restraints weight = 201483.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.160964 restraints weight = 141953.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.161471 restraints weight = 110301.728| |-----------------------------------------------------------------------------| r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5473 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 59216 Z= 0.175 Angle : 0.610 13.007 79948 Z= 0.303 Chirality : 0.043 0.235 9610 Planarity : 0.004 0.080 10225 Dihedral : 4.700 64.142 8179 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.02 % Allowed : 0.25 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.10), residues: 7598 helix: 0.56 (0.08), residues: 3917 sheet: -1.26 (0.19), residues: 725 loop : -1.15 (0.11), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 474 HIS 0.008 0.001 HIS d 347 PHE 0.022 0.001 PHE q 103 TYR 0.042 0.001 TYR h 419 ARG 0.008 0.000 ARG a 390 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16833.67 seconds wall clock time: 290 minutes 29.87 seconds (17429.87 seconds total)