Starting phenix.real_space_refine on Tue Mar 12 02:03:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6krd_0756/03_2024/6krd_0756.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6krd_0756/03_2024/6krd_0756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6krd_0756/03_2024/6krd_0756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6krd_0756/03_2024/6krd_0756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6krd_0756/03_2024/6krd_0756.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6krd_0756/03_2024/6krd_0756.pdb" } resolution = 4.38 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= 0.027 sd= 0.214 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 311 5.16 5 C 38287 2.51 5 N 10565 2.21 5 O 11842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "z ARG 15": "NH1" <-> "NH2" Residue "Z TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 61005 Number of models: 1 Model: "" Number of chains: 16 Chain: "a" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3851 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 10, 'TRANS': 500} Chain breaks: 1 Chain: "A" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3865 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 10, 'TRANS': 502} Chain breaks: 1 Chain: "b" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3811 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 10, 'TRANS': 491} Chain: "B" Number of atoms: 3824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3824 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 10, 'TRANS': 493} Chain: "d" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3655 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 467} Chain breaks: 2 Chain: "D" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3255 Classifications: {'peptide': 429} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 418} Chain breaks: 4 Chain: "e" Number of atoms: 3839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3839 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 15, 'TRANS': 485} Chain breaks: 1 Chain: "E" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3786 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 15, 'TRANS': 479} Chain breaks: 1 Chain: "g" Number of atoms: 3769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3769 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 19, 'TRANS': 473} Chain breaks: 1 Chain: "G" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3518 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 18, 'TRANS': 443} Chain breaks: 2 Chain: "q" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3978 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 18, 'TRANS': 505} Chain: "Q" Number of atoms: 3974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3974 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 18, 'TRANS': 504} Chain: "z" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4030 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 15, 'TRANS': 508} Chain breaks: 1 Chain: "Z" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4086 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 15, 'TRANS': 515} Chain: "h" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3882 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 12, 'TRANS': 494} Chain: "H" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3882 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 12, 'TRANS': 494} Time building chain proxies: 23.09, per 1000 atoms: 0.38 Number of scatterers: 61005 At special positions: 0 Unit cell: (199.018, 199.018, 192.428, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 311 16.00 O 11842 8.00 N 10565 7.00 C 38287 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.90 Conformation dependent library (CDL) restraints added in 8.4 seconds 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14896 Finding SS restraints... Secondary structure from input PDB file: 321 helices and 90 sheets defined 53.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.73 Creating SS restraints... Processing helix chain 'a' and resid 22 through 41 removed outlier: 3.754A pdb=" N ARG a 26 " --> pdb=" O GLY a 22 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL a 39 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL a 40 " --> pdb=" O VAL a 36 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 44 No H-bonds generated for 'chain 'a' and resid 42 through 44' Processing helix chain 'a' and resid 66 through 73 removed outlier: 3.905A pdb=" N LEU a 70 " --> pdb=" O GLY a 66 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER a 71 " --> pdb=" O ALA a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 94 removed outlier: 3.671A pdb=" N ILE a 82 " --> pdb=" O PRO a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 111 removed outlier: 3.737A pdb=" N VAL a 102 " --> pdb=" O THR a 98 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU a 109 " --> pdb=" O ALA a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 118 removed outlier: 3.924A pdb=" N LEU a 115 " --> pdb=" O ARG a 111 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS a 117 " --> pdb=" O ASN a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 144 removed outlier: 3.605A pdb=" N ILE a 137 " --> pdb=" O LEU a 133 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG a 138 " --> pdb=" O ARG a 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE a 139 " --> pdb=" O GLU a 135 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU a 142 " --> pdb=" O ARG a 138 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL a 143 " --> pdb=" O PHE a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 164 removed outlier: 4.375A pdb=" N ALA a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS a 161 " --> pdb=" O ILE a 157 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR a 162 " --> pdb=" O ASN a 158 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER a 163 " --> pdb=" O ILE a 159 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 171 Processing helix chain 'a' and resid 172 through 187 removed outlier: 4.576A pdb=" N ASN a 178 " --> pdb=" O ASP a 174 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N MET a 179 " --> pdb=" O PHE a 175 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA a 186 " --> pdb=" O ASP a 182 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL a 187 " --> pdb=" O ALA a 183 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 216 removed outlier: 3.557A pdb=" N SER a 216 " --> pdb=" O ALA a 213 " (cutoff:3.500A) Processing helix chain 'a' and resid 277 through 292 removed outlier: 3.586A pdb=" N VAL a 281 " --> pdb=" O GLU a 277 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU a 283 " --> pdb=" O GLY a 279 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG a 284 " --> pdb=" O ILE a 280 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE a 288 " --> pdb=" O ARG a 284 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE a 289 " --> pdb=" O VAL a 285 " (cutoff:3.500A) Processing helix chain 'a' and resid 303 through 313 removed outlier: 3.792A pdb=" N GLU a 309 " --> pdb=" O LEU a 305 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE a 310 " --> pdb=" O CYS a 306 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU a 312 " --> pdb=" O LYS a 308 " (cutoff:3.500A) Processing helix chain 'a' and resid 324 through 334 removed outlier: 4.300A pdb=" N ARG a 328 " --> pdb=" O GLU a 324 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG a 331 " --> pdb=" O ARG a 327 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 415 removed outlier: 3.584A pdb=" N GLU a 397 " --> pdb=" O TYR a 393 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG a 400 " --> pdb=" O ASP a 396 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N HIS a 403 " --> pdb=" O GLU a 399 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP a 404 " --> pdb=" O ARG a 400 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL a 408 " --> pdb=" O ASP a 404 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL a 409 " --> pdb=" O SER a 405 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER a 415 " --> pdb=" O ARG a 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 423 through 437 removed outlier: 3.810A pdb=" N ILE a 431 " --> pdb=" O ALA a 427 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP a 434 " --> pdb=" O ASN a 430 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN a 435 " --> pdb=" O ILE a 431 " (cutoff:3.500A) Processing helix chain 'a' and resid 443 through 454 removed outlier: 4.124A pdb=" N ALA a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) Processing helix chain 'a' and resid 456 through 466 removed outlier: 3.630A pdb=" N ASN a 465 " --> pdb=" O THR a 461 " (cutoff:3.500A) Processing helix chain 'a' and resid 469 through 485 removed outlier: 3.529A pdb=" N TYR a 480 " --> pdb=" O LYS a 476 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA a 483 " --> pdb=" O SER a 479 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN a 485 " --> pdb=" O HIS a 481 " (cutoff:3.500A) Processing helix chain 'a' and resid 511 through 516 Processing helix chain 'a' and resid 521 through 540 removed outlier: 3.709A pdb=" N ALA a 537 " --> pdb=" O GLU a 533 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE a 538 " --> pdb=" O ALA a 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 42 removed outlier: 3.889A pdb=" N ARG A 26 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.819A pdb=" N ILE A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.748A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.655A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 144 removed outlier: 3.639A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.953A pdb=" N ALA A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 removed outlier: 4.260A pdb=" N ASP A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASP A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N MET A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.833A pdb=" N SER A 216 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 290 removed outlier: 3.536A pdb=" N ILE A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 removed outlier: 4.184A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 removed outlier: 3.573A pdb=" N ARG A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 415 removed outlier: 3.532A pdb=" N LEU A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 441 removed outlier: 3.673A pdb=" N ILE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 454 Processing helix chain 'A' and resid 456 through 463 Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.619A pdb=" N SER A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 521 through 540 removed outlier: 3.550A pdb=" N LEU A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing helix chain 'b' and resid 20 through 35 removed outlier: 4.402A pdb=" N ALA b 26 " --> pdb=" O ALA b 22 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL b 29 " --> pdb=" O GLY b 25 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU b 32 " --> pdb=" O ALA b 28 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL b 33 " --> pdb=" O VAL b 29 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER b 35 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 59 through 67 removed outlier: 3.542A pdb=" N ILE b 63 " --> pdb=" O ASP b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 88 removed outlier: 3.912A pdb=" N ASN b 79 " --> pdb=" O LYS b 75 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE b 80 " --> pdb=" O VAL b 76 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU b 87 " --> pdb=" O VAL b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 105 removed outlier: 3.801A pdb=" N THR b 96 " --> pdb=" O THR b 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 138 removed outlier: 3.552A pdb=" N ALA b 130 " --> pdb=" O LEU b 126 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS b 137 " --> pdb=" O ASP b 133 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA b 138 " --> pdb=" O ALA b 134 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 160 removed outlier: 3.537A pdb=" N PHE b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU b 151 " --> pdb=" O THR b 147 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU b 153 " --> pdb=" O PHE b 149 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE b 154 " --> pdb=" O ARG b 150 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS b 155 " --> pdb=" O GLU b 151 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA b 157 " --> pdb=" O LEU b 153 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR b 159 " --> pdb=" O HIS b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 168 removed outlier: 3.593A pdb=" N GLN b 168 " --> pdb=" O ILE b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 183 removed outlier: 3.725A pdb=" N PHE b 173 " --> pdb=" O ASP b 169 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU b 176 " --> pdb=" O HIS b 172 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA b 177 " --> pdb=" O PHE b 173 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE b 181 " --> pdb=" O ALA b 177 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU b 182 " --> pdb=" O THR b 178 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG b 183 " --> pdb=" O ASN b 179 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 191 No H-bonds generated for 'chain 'b' and resid 189 through 191' Processing helix chain 'b' and resid 202 through 206 Processing helix chain 'b' and resid 254 through 259 removed outlier: 3.528A pdb=" N LEU b 258 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA b 259 " --> pdb=" O THR b 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 254 through 259' Processing helix chain 'b' and resid 259 through 278 removed outlier: 3.503A pdb=" N GLU b 267 " --> pdb=" O LYS b 263 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS b 270 " --> pdb=" O ARG b 266 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASN b 271 " --> pdb=" O GLU b 267 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS b 272 " --> pdb=" O LYS b 268 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS b 275 " --> pdb=" O ASN b 271 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE b 276 " --> pdb=" O LYS b 272 " (cutoff:3.500A) Processing helix chain 'b' and resid 291 through 302 removed outlier: 3.673A pdb=" N ASP b 300 " --> pdb=" O GLN b 296 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU b 301 " --> pdb=" O LEU b 297 " (cutoff:3.500A) Processing helix chain 'b' and resid 311 through 322 removed outlier: 3.587A pdb=" N ALA b 318 " --> pdb=" O VAL b 314 " (cutoff:3.500A) Processing helix chain 'b' and resid 373 through 397 removed outlier: 3.765A pdb=" N LEU b 377 " --> pdb=" O THR b 373 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP b 386 " --> pdb=" O ARG b 382 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL b 390 " --> pdb=" O ASP b 386 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR b 395 " --> pdb=" O LEU b 391 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS b 396 " --> pdb=" O SER b 392 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 419 removed outlier: 3.699A pdb=" N SER b 412 " --> pdb=" O GLU b 408 " (cutoff:3.500A) Processing helix chain 'b' and resid 426 through 438 removed outlier: 3.618A pdb=" N ARG b 435 " --> pdb=" O GLU b 431 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA b 436 " --> pdb=" O ALA b 432 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG b 438 " --> pdb=" O ALA b 434 " (cutoff:3.500A) Processing helix chain 'b' and resid 438 through 448 Processing helix chain 'b' and resid 451 through 465 removed outlier: 3.520A pdb=" N LEU b 455 " --> pdb=" O ASP b 451 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER b 461 " --> pdb=" O SER b 457 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN b 465 " --> pdb=" O SER b 461 " (cutoff:3.500A) Processing helix chain 'b' and resid 482 through 486 Processing helix chain 'b' and resid 491 through 510 removed outlier: 3.717A pdb=" N VAL b 507 " --> pdb=" O GLU b 503 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG b 510 " --> pdb=" O GLU b 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 35 removed outlier: 3.536A pdb=" N ALA B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 25 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER B 35 " --> pdb=" O ASP B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 73 through 88 removed outlier: 3.999A pdb=" N LEU B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 83 " --> pdb=" O ASN B 79 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 112 removed outlier: 3.521A pdb=" N THR B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 138 removed outlier: 4.424A pdb=" N ILE B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 161 removed outlier: 3.726A pdb=" N PHE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 152 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.670A pdb=" N GLN B 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 180 removed outlier: 3.904A pdb=" N PHE B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 255 through 268 removed outlier: 4.197A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.621A pdb=" N SER B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.567A pdb=" N PHE B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP B 300 " --> pdb=" O GLN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.562A pdb=" N VAL B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 397 removed outlier: 3.745A pdb=" N LEU B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B 378 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 419 removed outlier: 3.619A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 438 removed outlier: 3.659A pdb=" N PHE B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.810A pdb=" N THR B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 464 removed outlier: 3.516A pdb=" N SER B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 491 through 510 removed outlier: 3.692A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'd' and resid 18 through 37 removed outlier: 3.552A pdb=" N VAL d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR d 37 " --> pdb=" O ASP d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 60 through 68 Processing helix chain 'd' and resid 76 through 89 removed outlier: 4.046A pdb=" N GLU d 80 " --> pdb=" O ARG d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 113 removed outlier: 3.846A pdb=" N VAL d 97 " --> pdb=" O THR d 93 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU d 108 " --> pdb=" O LEU d 104 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG d 109 " --> pdb=" O GLY d 105 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU d 110 " --> pdb=" O ALA d 106 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN d 112 " --> pdb=" O GLU d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 116 through 139 removed outlier: 3.531A pdb=" N ILE d 120 " --> pdb=" O HIS d 116 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP d 133 " --> pdb=" O LYS d 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 158 removed outlier: 3.595A pdb=" N ALA d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU d 158 " --> pdb=" O ALA d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 159 through 161 No H-bonds generated for 'chain 'd' and resid 159 through 161' Processing helix chain 'd' and resid 166 through 183 Proline residue: d 172 - end of helix removed outlier: 3.715A pdb=" N LYS d 180 " --> pdb=" O ASP d 176 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE d 181 " --> pdb=" O SER d 177 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP d 183 " --> pdb=" O LEU d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 194 removed outlier: 3.828A pdb=" N ASP d 193 " --> pdb=" O ASP d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 267 through 281 removed outlier: 3.676A pdb=" N ASN d 273 " --> pdb=" O ALA d 269 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE d 274 " --> pdb=" O TYR d 270 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE d 278 " --> pdb=" O ILE d 274 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA d 281 " --> pdb=" O LYS d 277 " (cutoff:3.500A) Processing helix chain 'd' and resid 298 through 309 removed outlier: 4.019A pdb=" N HIS d 303 " --> pdb=" O ASP d 299 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE d 304 " --> pdb=" O LEU d 300 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS d 307 " --> pdb=" O HIS d 303 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU d 308 " --> pdb=" O PHE d 304 " (cutoff:3.500A) Processing helix chain 'd' and resid 318 through 328 removed outlier: 4.353A pdb=" N GLU d 322 " --> pdb=" O ARG d 318 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE d 323 " --> pdb=" O GLU d 319 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS d 326 " --> pdb=" O GLU d 322 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY d 327 " --> pdb=" O PHE d 323 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU d 328 " --> pdb=" O LEU d 324 " (cutoff:3.500A) Processing helix chain 'd' and resid 383 through 407 removed outlier: 3.767A pdb=" N ILE d 387 " --> pdb=" O ASN d 383 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU d 389 " --> pdb=" O MET d 385 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP d 396 " --> pdb=" O ARG d 392 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE d 401 " --> pdb=" O ALA d 397 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU d 404 " --> pdb=" O VAL d 400 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL d 405 " --> pdb=" O ILE d 401 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS d 406 " --> pdb=" O ARG d 402 " (cutoff:3.500A) Processing helix chain 'd' and resid 415 through 429 removed outlier: 3.683A pdb=" N SER d 422 " --> pdb=" O GLU d 418 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG d 424 " --> pdb=" O GLU d 420 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS d 427 " --> pdb=" O ARG d 423 " (cutoff:3.500A) Processing helix chain 'd' and resid 430 through 432 No H-bonds generated for 'chain 'd' and resid 430 through 432' Processing helix chain 'd' and resid 435 through 447 removed outlier: 3.802A pdb=" N ILE d 439 " --> pdb=" O VAL d 435 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN d 441 " --> pdb=" O ALA d 437 " (cutoff:3.500A) Processing helix chain 'd' and resid 448 through 458 removed outlier: 3.553A pdb=" N ALA d 458 " --> pdb=" O LEU d 454 " (cutoff:3.500A) Processing helix chain 'd' and resid 461 through 472 removed outlier: 3.592A pdb=" N LYS d 472 " --> pdb=" O GLU d 468 " (cutoff:3.500A) Processing helix chain 'd' and resid 473 through 475 No H-bonds generated for 'chain 'd' and resid 473 through 475' Processing helix chain 'd' and resid 500 through 519 removed outlier: 4.080A pdb=" N SER d 504 " --> pdb=" O PRO d 500 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE d 508 " --> pdb=" O SER d 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 37 removed outlier: 3.753A pdb=" N ARG D 21 " --> pdb=" O PRO D 17 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR D 37 " --> pdb=" O ASP D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.551A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 113 removed outlier: 3.547A pdb=" N ILE D 98 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 139 removed outlier: 3.551A pdb=" N ILE D 120 " --> pdb=" O HIS D 116 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET D 138 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 removed outlier: 4.158A pdb=" N LEU D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 156 " --> pdb=" O ARG D 152 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.816A pdb=" N SER D 168 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 183 removed outlier: 3.573A pdb=" N ALA D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASP D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 308 removed outlier: 3.535A pdb=" N HIS D 303 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS D 307 " --> pdb=" O HIS D 303 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU D 308 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 4.572A pdb=" N GLU D 322 " --> pdb=" O ARG D 318 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY D 327 " --> pdb=" O PHE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 407 removed outlier: 3.935A pdb=" N ILE D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.736A pdb=" N ILE D 419 " --> pdb=" O GLY D 415 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 434 through 447 removed outlier: 4.142A pdb=" N PHE D 438 " --> pdb=" O GLY D 434 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP D 440 " --> pdb=" O GLN D 436 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 447 " --> pdb=" O PHE D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.525A pdb=" N ALA D 458 " --> pdb=" O LEU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 476 removed outlier: 3.602A pdb=" N VAL D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU D 474 " --> pdb=" O ARG D 470 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN D 475 " --> pdb=" O SER D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 520 removed outlier: 3.582A pdb=" N ILE D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) Processing helix chain 'e' and resid 43 through 62 removed outlier: 3.662A pdb=" N LYS e 47 " --> pdb=" O GLY e 43 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS e 48 " --> pdb=" O LEU e 44 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE e 51 " --> pdb=" O LYS e 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU e 52 " --> pdb=" O LYS e 48 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL e 57 " --> pdb=" O ALA e 53 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE e 60 " --> pdb=" O SER e 56 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE e 61 " --> pdb=" O VAL e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 93 Processing helix chain 'e' and resid 101 through 115 removed outlier: 4.154A pdb=" N VAL e 105 " --> pdb=" O ALA e 101 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER e 110 " --> pdb=" O GLN e 106 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU e 114 " --> pdb=" O SER e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 118 through 139 removed outlier: 3.537A pdb=" N VAL e 124 " --> pdb=" O THR e 120 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU e 135 " --> pdb=" O ASP e 131 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU e 136 " --> pdb=" O GLN e 132 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 164 removed outlier: 3.628A pdb=" N ILE e 146 " --> pdb=" O HIS e 142 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP e 151 " --> pdb=" O ALA e 147 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU e 152 " --> pdb=" O ASN e 148 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER e 159 " --> pdb=" O LYS e 155 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS e 160 " --> pdb=" O LEU e 156 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR e 164 " --> pdb=" O LYS e 160 " (cutoff:3.500A) Processing helix chain 'e' and resid 175 through 188 removed outlier: 3.649A pdb=" N LEU e 180 " --> pdb=" O PHE e 176 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA e 184 " --> pdb=" O LEU e 180 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS e 185 " --> pdb=" O LEU e 181 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR e 186 " --> pdb=" O ARG e 182 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER e 187 " --> pdb=" O ALA e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 195 Processing helix chain 'e' and resid 196 through 211 removed outlier: 4.411A pdb=" N GLU e 202 " --> pdb=" O ASP e 198 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET e 203 " --> pdb=" O ARG e 199 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA e 204 " --> pdb=" O PHE e 200 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL e 205 " --> pdb=" O ALA e 201 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU e 206 " --> pdb=" O GLU e 202 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA e 207 " --> pdb=" O MET e 203 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL e 208 " --> pdb=" O ALA e 204 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL e 211 " --> pdb=" O ALA e 207 " (cutoff:3.500A) Processing helix chain 'e' and resid 220 through 222 No H-bonds generated for 'chain 'e' and resid 220 through 222' Processing helix chain 'e' and resid 233 through 237 removed outlier: 3.767A pdb=" N ASP e 236 " --> pdb=" O SER e 233 " (cutoff:3.500A) Processing helix chain 'e' and resid 306 through 317 removed outlier: 3.631A pdb=" N ASP e 311 " --> pdb=" O LYS e 307 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL e 313 " --> pdb=" O MET e 309 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA e 316 " --> pdb=" O ASP e 312 " (cutoff:3.500A) Processing helix chain 'e' and resid 328 through 338 removed outlier: 3.774A pdb=" N LEU e 334 " --> pdb=" O GLU e 330 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU e 335 " --> pdb=" O ALA e 331 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN e 337 " --> pdb=" O HIS e 333 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN e 338 " --> pdb=" O LEU e 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 353 through 359 Processing helix chain 'e' and resid 412 through 436 removed outlier: 3.508A pdb=" N ARG e 421 " --> pdb=" O ASP e 417 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP e 436 " --> pdb=" O ASN e 432 " (cutoff:3.500A) Processing helix chain 'e' and resid 444 through 458 removed outlier: 3.518A pdb=" N VAL e 448 " --> pdb=" O GLY e 444 " (cutoff:3.500A) Processing helix chain 'e' and resid 464 through 477 removed outlier: 3.952A pdb=" N ALA e 468 " --> pdb=" O ILE e 464 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP e 477 " --> pdb=" O ALA e 473 " (cutoff:3.500A) Processing helix chain 'e' and resid 477 through 487 Processing helix chain 'e' and resid 490 through 502 Processing helix chain 'e' and resid 521 through 526 removed outlier: 3.866A pdb=" N GLU e 524 " --> pdb=" O ASP e 521 " (cutoff:3.500A) Processing helix chain 'e' and resid 531 through 550 Processing helix chain 'E' and resid 45 through 59 removed outlier: 3.732A pdb=" N ILE E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 4.219A pdb=" N THR E 63 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU E 65 " --> pdb=" O LYS E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 93 removed outlier: 3.779A pdb=" N ILE E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 115 removed outlier: 4.039A pdb=" N VAL E 105 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER E 110 " --> pdb=" O GLN E 106 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP E 112 " --> pdb=" O SER E 108 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 139 removed outlier: 3.806A pdb=" N VAL E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU E 135 " --> pdb=" O ASP E 131 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN E 138 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 165 removed outlier: 3.541A pdb=" N ASP E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER E 159 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 182 removed outlier: 3.793A pdb=" N ARG E 177 " --> pdb=" O ASP E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.700A pdb=" N THR E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 195 Processing helix chain 'E' and resid 196 through 202 removed outlier: 3.778A pdb=" N PHE E 200 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 212 removed outlier: 4.090A pdb=" N GLU E 206 " --> pdb=" O GLU E 202 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE E 209 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN E 210 " --> pdb=" O GLU E 206 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 211 " --> pdb=" O ALA E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 317 removed outlier: 3.596A pdb=" N VAL E 313 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS E 314 " --> pdb=" O ILE E 310 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 333 through 338 removed outlier: 3.847A pdb=" N GLN E 337 " --> pdb=" O HIS E 333 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN E 338 " --> pdb=" O LEU E 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 333 through 338' Processing helix chain 'E' and resid 351 through 358 removed outlier: 3.976A pdb=" N ALA E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 436 removed outlier: 3.505A pdb=" N ASP E 425 " --> pdb=" O ARG E 421 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS E 428 " --> pdb=" O HIS E 424 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL E 430 " --> pdb=" O SER E 426 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 459 removed outlier: 3.563A pdb=" N VAL E 448 " --> pdb=" O GLY E 444 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 477 removed outlier: 3.560A pdb=" N ALA E 468 " --> pdb=" O ILE E 464 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP E 477 " --> pdb=" O ALA E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 487 Processing helix chain 'E' and resid 490 through 502 removed outlier: 3.607A pdb=" N THR E 497 " --> pdb=" O GLY E 493 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN E 502 " --> pdb=" O LEU E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 550 removed outlier: 3.549A pdb=" N GLN E 537 " --> pdb=" O GLY E 533 " (cutoff:3.500A) Processing helix chain 'g' and resid 18 through 35 removed outlier: 4.110A pdb=" N VAL g 34 " --> pdb=" O ALA g 30 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE g 35 " --> pdb=" O VAL g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 66 removed outlier: 3.535A pdb=" N ILE g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG g 66 " --> pdb=" O HIS g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 72 through 89 removed outlier: 4.003A pdb=" N LYS g 76 " --> pdb=" O HIS g 72 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER g 77 " --> pdb=" O PRO g 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 107 removed outlier: 3.534A pdb=" N VAL g 96 " --> pdb=" O GLY g 92 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE g 97 " --> pdb=" O THR g 93 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE g 103 " --> pdb=" O LEU g 99 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA g 105 " --> pdb=" O GLY g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 107 through 112 Processing helix chain 'g' and resid 117 through 140 Processing helix chain 'g' and resid 149 through 156 removed outlier: 4.212A pdb=" N LYS g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU g 154 " --> pdb=" O ALA g 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 157 through 159 No H-bonds generated for 'chain 'g' and resid 157 through 159' Processing helix chain 'g' and resid 162 through 166 removed outlier: 4.121A pdb=" N HIS g 166 " --> pdb=" O TYR g 163 " (cutoff:3.500A) Processing helix chain 'g' and resid 167 through 183 removed outlier: 4.211A pdb=" N GLU g 173 " --> pdb=" O GLU g 169 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU g 174 " --> pdb=" O LYS g 170 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA g 178 " --> pdb=" O LEU g 174 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL g 182 " --> pdb=" O ALA g 178 " (cutoff:3.500A) Processing helix chain 'g' and resid 276 through 288 removed outlier: 3.622A pdb=" N VAL g 280 " --> pdb=" O GLU g 276 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE g 287 " --> pdb=" O MET g 283 " (cutoff:3.500A) Processing helix chain 'g' and resid 289 through 291 No H-bonds generated for 'chain 'g' and resid 289 through 291' Processing helix chain 'g' and resid 302 through 311 removed outlier: 3.516A pdb=" N GLN g 306 " --> pdb=" O SER g 302 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS g 307 " --> pdb=" O ASP g 303 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR g 308 " --> pdb=" O LEU g 304 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS g 311 " --> pdb=" O HIS g 307 " (cutoff:3.500A) Processing helix chain 'g' and resid 324 through 333 removed outlier: 3.583A pdb=" N ARG g 330 " --> pdb=" O ASN g 326 " (cutoff:3.500A) Processing helix chain 'g' and resid 339 through 343 Processing helix chain 'g' and resid 385 through 409 removed outlier: 3.768A pdb=" N ARG g 394 " --> pdb=" O ASN g 390 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER g 409 " --> pdb=" O ASN g 405 " (cutoff:3.500A) Processing helix chain 'g' and resid 417 through 431 removed outlier: 3.561A pdb=" N SER g 424 " --> pdb=" O GLU g 420 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS g 426 " --> pdb=" O ALA g 422 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA g 428 " --> pdb=" O SER g 424 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU g 429 " --> pdb=" O VAL g 425 " (cutoff:3.500A) Processing helix chain 'g' and resid 438 through 450 removed outlier: 3.774A pdb=" N VAL g 445 " --> pdb=" O PRO g 441 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA g 446 " --> pdb=" O TYR g 442 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP g 447 " --> pdb=" O GLN g 443 " (cutoff:3.500A) Processing helix chain 'g' and resid 450 through 461 Processing helix chain 'g' and resid 463 through 478 removed outlier: 3.502A pdb=" N GLN g 470 " --> pdb=" O ARG g 466 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA g 473 " --> pdb=" O SER g 469 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS g 475 " --> pdb=" O LEU g 471 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA g 476 " --> pdb=" O ARG g 472 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN g 477 " --> pdb=" O ALA g 473 " (cutoff:3.500A) Processing helix chain 'g' and resid 503 through 523 removed outlier: 3.508A pdb=" N LEU g 521 " --> pdb=" O ALA g 517 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL g 523 " --> pdb=" O LEU g 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 35 removed outlier: 3.533A pdb=" N ILE G 22 " --> pdb=" O ARG G 18 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA G 28 " --> pdb=" O ASN G 24 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 39 removed outlier: 3.860A pdb=" N LEU G 39 " --> pdb=" O ARG G 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 36 through 39' Processing helix chain 'G' and resid 60 through 68 removed outlier: 3.739A pdb=" N ARG G 66 " --> pdb=" O HIS G 62 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 89 removed outlier: 3.860A pdb=" N LYS G 76 " --> pdb=" O HIS G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 107 removed outlier: 3.621A pdb=" N VAL G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 112 Processing helix chain 'G' and resid 117 through 140 removed outlier: 3.779A pdb=" N THR G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 157 removed outlier: 3.529A pdb=" N LYS G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS G 153 " --> pdb=" O ALA G 149 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA G 157 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 166 removed outlier: 4.159A pdb=" N HIS G 166 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 183 removed outlier: 3.784A pdb=" N GLU G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 198 removed outlier: 3.566A pdb=" N GLU G 197 " --> pdb=" O PRO G 194 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE G 198 " --> pdb=" O ASN G 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 194 through 198' Processing helix chain 'G' and resid 303 through 309 removed outlier: 4.239A pdb=" N HIS G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR G 308 " --> pdb=" O LEU G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 332 removed outlier: 3.588A pdb=" N ALA G 329 " --> pdb=" O ASN G 325 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL G 331 " --> pdb=" O ARG G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 408 removed outlier: 3.713A pdb=" N GLU G 391 " --> pdb=" O ASP G 387 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG G 394 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL G 402 " --> pdb=" O ASP G 398 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA G 403 " --> pdb=" O ALA G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 432 removed outlier: 3.539A pdb=" N VAL G 423 " --> pdb=" O THR G 419 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER G 424 " --> pdb=" O GLU G 420 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS G 426 " --> pdb=" O ALA G 422 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU G 429 " --> pdb=" O VAL G 425 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS G 432 " --> pdb=" O ALA G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 450 removed outlier: 3.549A pdb=" N TYR G 442 " --> pdb=" O GLN G 438 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN G 443 " --> pdb=" O GLN G 439 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA G 444 " --> pdb=" O TRP G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 460 removed outlier: 3.616A pdb=" N LEU G 456 " --> pdb=" O ILE G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 478 removed outlier: 3.560A pdb=" N LEU G 468 " --> pdb=" O PRO G 464 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER G 469 " --> pdb=" O ILE G 465 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS G 475 " --> pdb=" O LEU G 471 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA G 476 " --> pdb=" O ARG G 472 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN G 477 " --> pdb=" O ALA G 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 522 removed outlier: 3.617A pdb=" N LEU G 521 " --> pdb=" O ALA G 517 " (cutoff:3.500A) Processing helix chain 'q' and resid 27 through 44 removed outlier: 3.605A pdb=" N ILE q 32 " --> pdb=" O ILE q 28 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU q 38 " --> pdb=" O ALA q 34 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N MET q 41 " --> pdb=" O GLU q 37 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS q 42 " --> pdb=" O LEU q 38 " (cutoff:3.500A) Processing helix chain 'q' and resid 67 through 75 removed outlier: 3.660A pdb=" N ARG q 73 " --> pdb=" O ALA q 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU q 74 " --> pdb=" O THR q 70 " (cutoff:3.500A) Processing helix chain 'q' and resid 79 through 95 removed outlier: 3.611A pdb=" N LYS q 83 " --> pdb=" O HIS q 79 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU q 85 " --> pdb=" O ALA q 81 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN q 92 " --> pdb=" O ALA q 88 " (cutoff:3.500A) Processing helix chain 'q' and resid 99 through 121 removed outlier: 3.749A pdb=" N LEU q 111 " --> pdb=" O ALA q 107 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN q 112 " --> pdb=" O GLY q 108 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS q 116 " --> pdb=" O ASN q 112 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU q 117 " --> pdb=" O VAL q 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 123 through 142 removed outlier: 3.567A pdb=" N ILE q 127 " --> pdb=" O SER q 123 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) Processing helix chain 'q' and resid 159 through 168 Proline residue: q 165 - end of helix Processing helix chain 'q' and resid 176 through 190 removed outlier: 4.215A pdb=" N GLU q 180 " --> pdb=" O ASP q 176 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU q 181 " --> pdb=" O ILE q 177 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER q 187 " --> pdb=" O SER q 183 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS q 188 " --> pdb=" O GLU q 184 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL q 189 " --> pdb=" O ALA q 185 " (cutoff:3.500A) Processing helix chain 'q' and resid 270 through 294 removed outlier: 4.264A pdb=" N LEU q 274 " --> pdb=" O ALA q 270 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP q 275 " --> pdb=" O GLN q 271 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU q 290 " --> pdb=" O ALA q 286 " (cutoff:3.500A) Processing helix chain 'q' and resid 308 through 316 removed outlier: 3.962A pdb=" N TYR q 312 " --> pdb=" O LEU q 308 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU q 313 " --> pdb=" O ALA q 309 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN q 314 " --> pdb=" O LEU q 310 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG q 315 " --> pdb=" O HIS q 311 " (cutoff:3.500A) Processing helix chain 'q' and resid 325 through 334 removed outlier: 4.008A pdb=" N LEU q 329 " --> pdb=" O SER q 325 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG q 330 " --> pdb=" O LYS q 326 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG q 331 " --> pdb=" O PHE q 327 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU q 332 " --> pdb=" O GLU q 328 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG q 334 " --> pdb=" O ARG q 330 " (cutoff:3.500A) Processing helix chain 'q' and resid 391 through 410 removed outlier: 3.685A pdb=" N ASP q 395 " --> pdb=" O GLN q 391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP q 396 " --> pdb=" O ASN q 392 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP q 402 " --> pdb=" O GLU q 398 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP q 403 " --> pdb=" O ARG q 399 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA q 406 " --> pdb=" O ASP q 402 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA q 407 " --> pdb=" O ASP q 403 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL q 408 " --> pdb=" O GLY q 404 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS q 409 " --> pdb=" O VAL q 405 " (cutoff:3.500A) Processing helix chain 'q' and resid 424 through 439 removed outlier: 3.579A pdb=" N ILE q 428 " --> pdb=" O GLY q 424 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE q 431 " --> pdb=" O GLU q 427 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER q 432 " --> pdb=" O ILE q 428 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG q 433 " --> pdb=" O GLU q 429 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR q 437 " --> pdb=" O ARG q 433 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU q 439 " --> pdb=" O THR q 435 " (cutoff:3.500A) Processing helix chain 'q' and resid 445 through 455 Processing helix chain 'q' and resid 457 through 467 Processing helix chain 'q' and resid 470 through 483 removed outlier: 3.560A pdb=" N LEU q 475 " --> pdb=" O VAL q 471 " (cutoff:3.500A) Proline residue: q 476 - end of helix removed outlier: 3.563A pdb=" N TYR q 479 " --> pdb=" O LEU q 475 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS q 482 " --> pdb=" O LEU q 478 " (cutoff:3.500A) Processing helix chain 'q' and resid 511 through 515 removed outlier: 3.688A pdb=" N GLU q 514 " --> pdb=" O ASP q 511 " (cutoff:3.500A) Processing helix chain 'q' and resid 521 through 541 removed outlier: 3.679A pdb=" N ASN q 529 " --> pdb=" O LYS q 525 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL q 538 " --> pdb=" O ALA q 534 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 44 removed outlier: 3.765A pdb=" N LEU Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN Q 40 " --> pdb=" O ARG Q 36 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N MET Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N CYS Q 42 " --> pdb=" O LEU Q 38 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 75 removed outlier: 3.671A pdb=" N MET Q 71 " --> pdb=" O ASP Q 67 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 95 removed outlier: 4.091A pdb=" N LEU Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN Q 91 " --> pdb=" O MET Q 87 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 114 removed outlier: 3.954A pdb=" N MET Q 104 " --> pdb=" O THR Q 100 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE Q 105 " --> pdb=" O ASN Q 101 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU Q 111 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN Q 112 " --> pdb=" O GLY Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 120 Processing helix chain 'Q' and resid 123 through 142 removed outlier: 3.712A pdb=" N ILE Q 127 " --> pdb=" O SER Q 123 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS Q 136 " --> pdb=" O ASN Q 132 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE Q 137 " --> pdb=" O MET Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 168 Proline residue: Q 165 - end of helix Processing helix chain 'Q' and resid 174 through 190 removed outlier: 4.280A pdb=" N GLU Q 180 " --> pdb=" O ASP Q 176 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU Q 181 " --> pdb=" O ILE Q 177 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL Q 182 " --> pdb=" O LEU Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 294 removed outlier: 4.034A pdb=" N LEU Q 274 " --> pdb=" O ALA Q 270 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP Q 275 " --> pdb=" O GLN Q 271 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU Q 281 " --> pdb=" O SER Q 277 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS Q 282 " --> pdb=" O LYS Q 278 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU Q 290 " --> pdb=" O ALA Q 286 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET Q 294 " --> pdb=" O GLU Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 316 removed outlier: 3.907A pdb=" N LEU Q 310 " --> pdb=" O GLY Q 306 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS Q 311 " --> pdb=" O GLU Q 307 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR Q 312 " --> pdb=" O LEU Q 308 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU Q 313 " --> pdb=" O ALA Q 309 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN Q 314 " --> pdb=" O LEU Q 310 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG Q 315 " --> pdb=" O HIS Q 311 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR Q 316 " --> pdb=" O TYR Q 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 306 through 316' Processing helix chain 'Q' and resid 326 through 333 removed outlier: 4.287A pdb=" N ARG Q 330 " --> pdb=" O LYS Q 326 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG Q 331 " --> pdb=" O PHE Q 327 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS Q 333 " --> pdb=" O LEU Q 329 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 352 Processing helix chain 'Q' and resid 390 through 407 removed outlier: 3.638A pdb=" N LEU Q 394 " --> pdb=" O THR Q 390 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP Q 395 " --> pdb=" O GLN Q 391 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP Q 396 " --> pdb=" O ASN Q 392 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA Q 407 " --> pdb=" O ASP Q 403 " (cutoff:3.500A) Processing helix chain 'Q' and resid 408 through 412 removed outlier: 3.703A pdb=" N MET Q 412 " --> pdb=" O LYS Q 409 " (cutoff:3.500A) Processing helix chain 'Q' and resid 424 through 441 removed outlier: 3.701A pdb=" N ILE Q 428 " --> pdb=" O GLY Q 424 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE Q 431 " --> pdb=" O GLU Q 427 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER Q 432 " --> pdb=" O ILE Q 428 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG Q 433 " --> pdb=" O GLU Q 429 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU Q 439 " --> pdb=" O THR Q 435 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG Q 440 " --> pdb=" O LYS Q 436 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 455 removed outlier: 4.424A pdb=" N ALA Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 467 Processing helix chain 'Q' and resid 470 through 483 removed outlier: 3.624A pdb=" N VAL Q 474 " --> pdb=" O ASP Q 470 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU Q 475 " --> pdb=" O VAL Q 471 " (cutoff:3.500A) Proline residue: Q 476 - end of helix Processing helix chain 'Q' and resid 511 through 516 Processing helix chain 'Q' and resid 521 through 541 removed outlier: 3.522A pdb=" N PHE Q 526 " --> pdb=" O ALA Q 522 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN Q 529 " --> pdb=" O LYS Q 525 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR Q 537 " --> pdb=" O GLU Q 533 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL Q 538 " --> pdb=" O ALA Q 534 " (cutoff:3.500A) Processing helix chain 'z' and resid 18 through 35 removed outlier: 3.632A pdb=" N VAL z 32 " --> pdb=" O GLY z 28 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR z 35 " --> pdb=" O SER z 31 " (cutoff:3.500A) Processing helix chain 'z' and resid 58 through 65 Processing helix chain 'z' and resid 71 through 86 removed outlier: 4.045A pdb=" N LEU z 75 " --> pdb=" O PRO z 71 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE z 76 " --> pdb=" O THR z 72 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA z 81 " --> pdb=" O ALA z 77 " (cutoff:3.500A) Processing helix chain 'z' and resid 90 through 108 removed outlier: 3.725A pdb=" N VAL z 95 " --> pdb=" O THR z 91 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG z 107 " --> pdb=" O ARG z 103 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE z 108 " --> pdb=" O GLN z 104 " (cutoff:3.500A) Processing helix chain 'z' and resid 114 through 137 removed outlier: 3.856A pdb=" N LYS z 131 " --> pdb=" O LYS z 127 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE z 132 " --> pdb=" O GLU z 128 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU z 135 " --> pdb=" O LYS z 131 " (cutoff:3.500A) Processing helix chain 'z' and resid 143 through 145 No H-bonds generated for 'chain 'z' and resid 143 through 145' Processing helix chain 'z' and resid 146 through 162 removed outlier: 4.123A pdb=" N GLN z 152 " --> pdb=" O GLU z 148 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER z 156 " --> pdb=" O GLN z 152 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER z 157 " --> pdb=" O VAL z 153 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR z 160 " --> pdb=" O SER z 156 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS z 161 " --> pdb=" O SER z 157 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL z 162 " --> pdb=" O LEU z 158 " (cutoff:3.500A) Processing helix chain 'z' and resid 166 through 182 Proline residue: z 172 - end of helix removed outlier: 3.937A pdb=" N VAL z 178 " --> pdb=" O VAL z 174 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU z 179 " --> pdb=" O THR z 175 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL z 181 " --> pdb=" O ALA z 177 " (cutoff:3.500A) Processing helix chain 'z' and resid 203 through 207 removed outlier: 3.528A pdb=" N THR z 207 " --> pdb=" O PRO z 204 " (cutoff:3.500A) Processing helix chain 'z' and resid 263 through 284 removed outlier: 4.779A pdb=" N PHE z 269 " --> pdb=" O SER z 265 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL z 270 " --> pdb=" O GLU z 266 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS z 273 " --> pdb=" O PHE z 269 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS z 276 " --> pdb=" O ALA z 272 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP z 279 " --> pdb=" O LYS z 275 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU z 280 " --> pdb=" O LYS z 276 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS z 281 " --> pdb=" O ILE z 277 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN z 282 " --> pdb=" O ILE z 278 " (cutoff:3.500A) Processing helix chain 'z' and resid 303 through 312 removed outlier: 4.374A pdb=" N ASP z 307 " --> pdb=" O PRO z 303 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL z 308 " --> pdb=" O MET z 304 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS z 311 " --> pdb=" O ASP z 307 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS z 312 " --> pdb=" O VAL z 308 " (cutoff:3.500A) Processing helix chain 'z' and resid 321 through 332 removed outlier: 3.518A pdb=" N GLU z 326 " --> pdb=" O ARG z 322 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG z 327 " --> pdb=" O ARG z 323 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN z 329 " --> pdb=" O MET z 325 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU z 330 " --> pdb=" O GLU z 326 " (cutoff:3.500A) Processing helix chain 'z' and resid 344 through 348 removed outlier: 3.745A pdb=" N LEU z 348 " --> pdb=" O PRO z 345 " (cutoff:3.500A) Processing helix chain 'z' and resid 384 through 408 removed outlier: 3.717A pdb=" N LEU z 388 " --> pdb=" O THR z 384 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN z 404 " --> pdb=" O ARG z 400 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL z 405 " --> pdb=" O ALA z 401 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU z 406 " --> pdb=" O VAL z 402 " (cutoff:3.500A) Processing helix chain 'z' and resid 416 through 434 removed outlier: 3.545A pdb=" N ARG z 427 " --> pdb=" O SER z 423 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN z 430 " --> pdb=" O LEU z 426 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET z 431 " --> pdb=" O ARG z 427 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN z 432 " --> pdb=" O SER z 428 " (cutoff:3.500A) Processing helix chain 'z' and resid 439 through 451 removed outlier: 4.222A pdb=" N GLY z 443 " --> pdb=" O LYS z 439 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA z 446 " --> pdb=" O THR z 442 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU z 451 " --> pdb=" O PHE z 447 " (cutoff:3.500A) Processing helix chain 'z' and resid 452 through 462 removed outlier: 3.517A pdb=" N LYS z 456 " --> pdb=" O LEU z 452 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL z 459 " --> pdb=" O PRO z 455 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER z 462 " --> pdb=" O LEU z 458 " (cutoff:3.500A) Processing helix chain 'z' and resid 465 through 483 removed outlier: 3.874A pdb=" N ASP z 479 " --> pdb=" O ASP z 475 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP z 482 " --> pdb=" O ASP z 478 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER z 483 " --> pdb=" O ASP z 479 " (cutoff:3.500A) Processing helix chain 'z' and resid 500 through 505 Processing helix chain 'z' and resid 510 through 529 removed outlier: 3.656A pdb=" N THR z 518 " --> pdb=" O ARG z 514 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU z 528 " --> pdb=" O ALA z 524 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 35 removed outlier: 3.539A pdb=" N LEU Z 29 " --> pdb=" O SER Z 25 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR Z 35 " --> pdb=" O SER Z 31 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 64 removed outlier: 3.600A pdb=" N LEU Z 62 " --> pdb=" O ASP Z 58 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR Z 64 " --> pdb=" O LYS Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 80 removed outlier: 3.840A pdb=" N LEU Z 75 " --> pdb=" O PRO Z 71 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE Z 76 " --> pdb=" O THR Z 72 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA Z 80 " --> pdb=" O ILE Z 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 87 removed outlier: 3.555A pdb=" N GLU Z 85 " --> pdb=" O ALA Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 111 removed outlier: 3.511A pdb=" N VAL Z 95 " --> pdb=" O THR Z 91 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Z 102 " --> pdb=" O VAL Z 98 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG Z 107 " --> pdb=" O ARG Z 103 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE Z 108 " --> pdb=" O GLN Z 104 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU Z 111 " --> pdb=" O ARG Z 107 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 137 removed outlier: 3.647A pdb=" N LYS Z 131 " --> pdb=" O LYS Z 127 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU Z 135 " --> pdb=" O LYS Z 131 " (cutoff:3.500A) Processing helix chain 'Z' and resid 143 through 145 No H-bonds generated for 'chain 'Z' and resid 143 through 145' Processing helix chain 'Z' and resid 146 through 162 removed outlier: 4.364A pdb=" N GLN Z 152 " --> pdb=" O GLU Z 148 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL Z 153 " --> pdb=" O PHE Z 149 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER Z 156 " --> pdb=" O GLN Z 152 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER Z 157 " --> pdb=" O VAL Z 153 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR Z 160 " --> pdb=" O SER Z 156 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS Z 161 " --> pdb=" O SER Z 157 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL Z 162 " --> pdb=" O LEU Z 158 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 182 Proline residue: Z 172 - end of helix removed outlier: 3.855A pdb=" N VAL Z 178 " --> pdb=" O VAL Z 174 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU Z 179 " --> pdb=" O THR Z 175 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER Z 180 " --> pdb=" O ASP Z 176 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL Z 181 " --> pdb=" O ALA Z 177 " (cutoff:3.500A) Processing helix chain 'Z' and resid 203 through 207 Processing helix chain 'Z' and resid 255 through 284 removed outlier: 3.557A pdb=" N ARG Z 259 " --> pdb=" O SER Z 255 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP Z 260 " --> pdb=" O ALA Z 256 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS Z 261 " --> pdb=" O ASP Z 257 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU Z 262 " --> pdb=" O GLN Z 258 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU Z 266 " --> pdb=" O LEU Z 262 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE Z 269 " --> pdb=" O SER Z 265 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL Z 270 " --> pdb=" O GLU Z 266 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS Z 273 " --> pdb=" O PHE Z 269 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS Z 276 " --> pdb=" O ALA Z 272 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU Z 280 " --> pdb=" O LYS Z 276 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS Z 281 " --> pdb=" O ILE Z 277 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN Z 282 " --> pdb=" O ILE Z 278 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL Z 284 " --> pdb=" O LEU Z 280 " (cutoff:3.500A) Processing helix chain 'Z' and resid 304 through 312 removed outlier: 3.940A pdb=" N VAL Z 308 " --> pdb=" O MET Z 304 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS Z 311 " --> pdb=" O ASP Z 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS Z 312 " --> pdb=" O VAL Z 308 " (cutoff:3.500A) Processing helix chain 'Z' and resid 321 through 332 removed outlier: 3.919A pdb=" N GLU Z 326 " --> pdb=" O ARG Z 322 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG Z 327 " --> pdb=" O ARG Z 323 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU Z 330 " --> pdb=" O GLU Z 326 " (cutoff:3.500A) Processing helix chain 'Z' and resid 344 through 348 removed outlier: 3.641A pdb=" N LEU Z 348 " --> pdb=" O PRO Z 345 " (cutoff:3.500A) Processing helix chain 'Z' and resid 385 through 408 removed outlier: 3.526A pdb=" N ALA Z 389 " --> pdb=" O HIS Z 385 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN Z 404 " --> pdb=" O ARG Z 400 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL Z 405 " --> pdb=" O ALA Z 401 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS Z 407 " --> pdb=" O ALA Z 403 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 434 removed outlier: 3.504A pdb=" N SER Z 428 " --> pdb=" O ARG Z 424 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN Z 430 " --> pdb=" O LEU Z 426 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N MET Z 431 " --> pdb=" O ARG Z 427 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN Z 432 " --> pdb=" O SER Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 440 through 451 Processing helix chain 'Z' and resid 452 through 463 removed outlier: 3.526A pdb=" N LYS Z 456 " --> pdb=" O LEU Z 452 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER Z 462 " --> pdb=" O LEU Z 458 " (cutoff:3.500A) Processing helix chain 'Z' and resid 465 through 483 removed outlier: 3.559A pdb=" N VAL Z 469 " --> pdb=" O ASP Z 465 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP Z 479 " --> pdb=" O ASP Z 475 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP Z 482 " --> pdb=" O ASP Z 478 " (cutoff:3.500A) Processing helix chain 'Z' and resid 500 through 505 Processing helix chain 'Z' and resid 510 through 529 removed outlier: 3.751A pdb=" N LEU Z 528 " --> pdb=" O ALA Z 524 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU Z 529 " --> pdb=" O SER Z 525 " (cutoff:3.500A) Processing helix chain 'h' and resid 23 through 41 removed outlier: 3.865A pdb=" N ILE h 27 " --> pdb=" O LYS h 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS h 33 " --> pdb=" O ASN h 29 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA h 35 " --> pdb=" O ASN h 31 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL h 36 " --> pdb=" O ALA h 32 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU h 40 " --> pdb=" O VAL h 36 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 72 removed outlier: 3.517A pdb=" N ILE h 69 " --> pdb=" O ASP h 65 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 94 removed outlier: 4.158A pdb=" N LEU h 83 " --> pdb=" O ALA h 79 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL h 84 " --> pdb=" O ALA h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 112 removed outlier: 3.784A pdb=" N THR h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU h 108 " --> pdb=" O LEU h 104 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N MET h 109 " --> pdb=" O ALA h 105 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 117 removed outlier: 3.751A pdb=" N GLU h 117 " --> pdb=" O LYS h 113 " (cutoff:3.500A) Processing helix chain 'h' and resid 121 through 144 removed outlier: 3.716A pdb=" N ILE h 125 " --> pdb=" O SER h 121 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG h 130 " --> pdb=" O MET h 126 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA h 132 " --> pdb=" O GLY h 128 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU h 135 " --> pdb=" O LYS h 131 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU h 138 " --> pdb=" O SER h 134 " (cutoff:3.500A) Processing helix chain 'h' and resid 153 through 166 removed outlier: 3.833A pdb=" N LEU h 158 " --> pdb=" O GLY h 154 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS h 161 " --> pdb=" O LEU h 157 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG h 163 " --> pdb=" O GLU h 159 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR h 164 " --> pdb=" O ARG h 160 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA h 165 " --> pdb=" O CYS h 161 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET h 166 " --> pdb=" O ALA h 162 " (cutoff:3.500A) Processing helix chain 'h' and resid 174 through 188 removed outlier: 3.564A pdb=" N PHE h 178 " --> pdb=" O ASN h 174 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS h 180 " --> pdb=" O ASP h 176 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET h 181 " --> pdb=" O PHE h 177 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP h 184 " --> pdb=" O LYS h 180 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL h 186 " --> pdb=" O CYS h 182 " (cutoff:3.500A) Processing helix chain 'h' and resid 195 through 197 No H-bonds generated for 'chain 'h' and resid 195 through 197' Processing helix chain 'h' and resid 268 through 273 removed outlier: 3.614A pdb=" N VAL h 271 " --> pdb=" O GLN h 268 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA h 273 " --> pdb=" O ILE h 270 " (cutoff:3.500A) Processing helix chain 'h' and resid 274 through 289 removed outlier: 3.687A pdb=" N ILE h 278 " --> pdb=" O GLU h 274 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG h 283 " --> pdb=" O PHE h 279 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL h 285 " --> pdb=" O LYS h 281 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU h 286 " --> pdb=" O LEU h 282 " (cutoff:3.500A) Processing helix chain 'h' and resid 302 through 307 removed outlier: 4.204A pdb=" N PHE h 306 " --> pdb=" O LEU h 302 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE h 307 " --> pdb=" O ALA h 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 302 through 307' Processing helix chain 'h' and resid 319 through 331 removed outlier: 3.543A pdb=" N ASN h 324 " --> pdb=" O ALA h 320 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG h 325 " --> pdb=" O ASP h 321 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN h 328 " --> pdb=" O ASN h 324 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL h 330 " --> pdb=" O VAL h 326 " (cutoff:3.500A) Processing helix chain 'h' and resid 342 through 346 Processing helix chain 'h' and resid 382 through 406 removed outlier: 3.534A pdb=" N ILE h 386 " --> pdb=" O ALA h 382 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP h 395 " --> pdb=" O ARG h 391 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA h 396 " --> pdb=" O SER h 392 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU h 404 " --> pdb=" O VAL h 400 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN h 405 " --> pdb=" O LYS h 401 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN h 406 " --> pdb=" O ARG h 402 " (cutoff:3.500A) Processing helix chain 'h' and resid 414 through 430 removed outlier: 3.643A pdb=" N SER h 421 " --> pdb=" O GLU h 417 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS h 422 " --> pdb=" O MET h 418 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS h 423 " --> pdb=" O GLU h 419 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP h 426 " --> pdb=" O LYS h 422 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS h 429 " --> pdb=" O ARG h 425 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR h 430 " --> pdb=" O ASP h 426 " (cutoff:3.500A) Processing helix chain 'h' and resid 434 through 446 removed outlier: 3.575A pdb=" N ILE h 438 " --> pdb=" O LYS h 434 " (cutoff:3.500A) Processing helix chain 'h' and resid 447 through 458 Processing helix chain 'h' and resid 460 through 473 removed outlier: 3.580A pdb=" N ILE h 464 " --> pdb=" O ASP h 460 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU h 465 " --> pdb=" O ALA h 461 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN h 466 " --> pdb=" O ILE h 462 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG h 469 " --> pdb=" O LEU h 465 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU h 470 " --> pdb=" O ASN h 466 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA h 471 " --> pdb=" O LYS h 467 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER h 473 " --> pdb=" O ARG h 469 " (cutoff:3.500A) Processing helix chain 'h' and resid 491 through 495 Processing helix chain 'h' and resid 500 through 518 removed outlier: 3.534A pdb=" N LEU h 507 " --> pdb=" O LYS h 503 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN h 508 " --> pdb=" O ILE h 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 41 removed outlier: 3.685A pdb=" N ALA H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 74 removed outlier: 3.556A pdb=" N LEU H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP H 74 " --> pdb=" O LEU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 94 removed outlier: 3.513A pdb=" N SER H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 112 removed outlier: 3.992A pdb=" N THR H 102 " --> pdb=" O THR H 98 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N MET H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 118 removed outlier: 3.935A pdb=" N GLU H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU H 118 " --> pdb=" O PRO H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 144 removed outlier: 3.640A pdb=" N ILE H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS H 131 " --> pdb=" O LYS H 127 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU H 138 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS H 139 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN H 141 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU H 142 " --> pdb=" O GLU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 166 removed outlier: 4.496A pdb=" N LEU H 158 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA H 162 " --> pdb=" O LEU H 158 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR H 164 " --> pdb=" O ARG H 160 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA H 165 " --> pdb=" O CYS H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 188 removed outlier: 4.115A pdb=" N LYS H 180 " --> pdb=" O ASP H 176 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET H 181 " --> pdb=" O PHE H 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP H 184 " --> pdb=" O LYS H 180 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 185 " --> pdb=" O MET H 181 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL H 186 " --> pdb=" O CYS H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 208 through 212 removed outlier: 3.590A pdb=" N GLU H 211 " --> pdb=" O ALA H 208 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER H 212 " --> pdb=" O MET H 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 208 through 212' Processing helix chain 'H' and resid 264 through 272 removed outlier: 3.741A pdb=" N GLN H 268 " --> pdb=" O GLU H 265 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA H 269 " --> pdb=" O ASP H 266 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE H 270 " --> pdb=" O TYR H 267 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL H 271 " --> pdb=" O GLN H 268 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP H 272 " --> pdb=" O ALA H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 280 Processing helix chain 'H' and resid 281 through 287 removed outlier: 3.566A pdb=" N VAL H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 310 Processing helix chain 'H' and resid 319 through 331 removed outlier: 3.537A pdb=" N MET H 323 " --> pdb=" O SER H 319 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN H 324 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG H 325 " --> pdb=" O ASP H 321 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL H 326 " --> pdb=" O ASP H 322 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE H 327 " --> pdb=" O MET H 323 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN H 328 " --> pdb=" O ASN H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 346 Processing helix chain 'H' and resid 382 through 406 removed outlier: 3.646A pdb=" N GLU H 388 " --> pdb=" O GLN H 384 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP H 395 " --> pdb=" O ARG H 391 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA H 396 " --> pdb=" O SER H 392 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE H 399 " --> pdb=" O ASP H 395 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU H 404 " --> pdb=" O VAL H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 431 removed outlier: 3.621A pdb=" N GLU H 419 " --> pdb=" O ALA H 415 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER H 421 " --> pdb=" O GLU H 417 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU H 424 " --> pdb=" O VAL H 420 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG H 425 " --> pdb=" O SER H 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP H 426 " --> pdb=" O LYS H 422 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS H 429 " --> pdb=" O ARG H 425 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR H 430 " --> pdb=" O ASP H 426 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE H 431 " --> pdb=" O TYR H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 446 Processing helix chain 'H' and resid 447 through 458 Processing helix chain 'H' and resid 460 through 472 removed outlier: 3.735A pdb=" N ARG H 469 " --> pdb=" O LEU H 465 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU H 470 " --> pdb=" O ASN H 466 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA H 471 " --> pdb=" O LYS H 467 " (cutoff:3.500A) Processing helix chain 'H' and resid 500 through 519 removed outlier: 3.741A pdb=" N LEU H 507 " --> pdb=" O LYS H 503 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN H 508 " --> pdb=" O ILE H 504 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE H 517 " --> pdb=" O ALA H 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 19 through 21 removed outlier: 3.589A pdb=" N ILE a 20 " --> pdb=" O MET a 544 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE a 541 " --> pdb=" O ASP d 45 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N MET d 47 " --> pdb=" O ILE a 541 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR a 543 " --> pdb=" O MET d 47 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LYS d 49 " --> pdb=" O THR a 543 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE a 545 " --> pdb=" O LYS d 49 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS d 46 " --> pdb=" O SER d 58 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER d 58 " --> pdb=" O LYS d 46 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE d 48 " --> pdb=" O ILE d 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE d 56 " --> pdb=" O ILE d 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 62 through 63 removed outlier: 4.389A pdb=" N THR a 63 " --> pdb=" O LYS a 51 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS a 51 " --> pdb=" O THR a 63 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL g 527 " --> pdb=" O MET a 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 204 through 207 removed outlier: 6.023A pdb=" N ASN a 204 " --> pdb=" O ILE a 385 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU a 387 " --> pdb=" O ASN a 204 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU a 206 " --> pdb=" O LEU a 387 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER a 384 " --> pdb=" O VAL a 219 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL a 219 " --> pdb=" O SER a 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'a' and resid 222 through 225 removed outlier: 7.668A pdb=" N GLY a 376 " --> pdb=" O ASP a 359 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 244 through 246 removed outlier: 3.659A pdb=" N LEU a 297 " --> pdb=" O ALA a 245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 418 through 420 Processing sheet with id=AA7, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.562A pdb=" N ILE A 20 " --> pdb=" O MET A 544 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 544 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR A 543 " --> pdb=" O MET D 47 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LYS D 49 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE A 545 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS D 46 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER D 58 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE D 48 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'A' and resid 205 through 208 removed outlier: 6.115A pdb=" N LEU A 206 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 384 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 219 " --> pdb=" O SER A 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 222 through 225 removed outlier: 3.783A pdb=" N LYS A 375 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 360 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR A 377 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N CYS A 358 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.546A pdb=" N THR A 298 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AB4, first strand: chain 'b' and resid 55 through 57 removed outlier: 3.763A pdb=" N MET b 55 " --> pdb=" O LEU b 46 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU b 46 " --> pdb=" O MET b 55 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR b 57 " --> pdb=" O LYS b 44 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS b 44 " --> pdb=" O THR b 57 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASP b 43 " --> pdb=" O ILE d 521 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP d 523 " --> pdb=" O ASP b 43 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU b 45 " --> pdb=" O ASP d 523 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA d 525 " --> pdb=" O LEU b 45 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 193 through 198 removed outlier: 6.304A pdb=" N GLN b 194 " --> pdb=" O ILE b 367 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU b 369 " --> pdb=" O GLN b 194 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE b 196 " --> pdb=" O LEU b 369 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 225 through 229 removed outlier: 6.954A pdb=" N ASP b 341 " --> pdb=" O ASN b 228 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N CYS b 340 " --> pdb=" O CYS b 359 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS b 359 " --> pdb=" O CYS b 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 231 through 233 removed outlier: 7.297A pdb=" N LEU b 232 " --> pdb=" O ILE b 285 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 400 through 402 Processing sheet with id=AB9, first strand: chain 'b' and resid 470 through 473 Processing sheet with id=AC1, first strand: chain 'B' and resid 55 through 57 removed outlier: 3.639A pdb=" N MET B 55 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR B 57 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS B 44 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP B 43 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASP D 523 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 45 " --> pdb=" O ASP D 523 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA D 525 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 47 " --> pdb=" O ALA D 525 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 193 through 199 removed outlier: 3.528A pdb=" N VAL B 368 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE B 207 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 212 through 215 removed outlier: 6.004A pdb=" N CYS B 359 " --> pdb=" O CYS B 340 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS B 340 " --> pdb=" O CYS B 359 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY B 338 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 342 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLU B 227 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N GLU B 344 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG B 225 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 283 through 285 Processing sheet with id=AC5, first strand: chain 'B' and resid 400 through 402 Processing sheet with id=AC6, first strand: chain 'B' and resid 470 through 473 Processing sheet with id=AC7, first strand: chain 'B' and resid 511 through 514 removed outlier: 8.027A pdb=" N ILE E 73 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE B 514 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N ILE E 75 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS E 72 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR E 84 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'd' and resid 197 through 200 removed outlier: 6.115A pdb=" N VAL d 197 " --> pdb=" O ILE d 379 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLY d 381 " --> pdb=" O VAL d 197 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS d 199 " --> pdb=" O GLY d 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'd' and resid 213 through 214 removed outlier: 3.673A pdb=" N VAL d 213 " --> pdb=" O VAL d 363 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL d 363 " --> pdb=" O VAL d 213 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ARG d 362 " --> pdb=" O VAL d 350 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL d 350 " --> pdb=" O ARG d 362 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR d 364 " --> pdb=" O ASP d 348 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP d 348 " --> pdb=" O LYS d 231 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 234 through 237 removed outlier: 4.295A pdb=" N GLY d 235 " --> pdb=" O VAL d 285 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU d 287 " --> pdb=" O GLY d 235 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN d 289 " --> pdb=" O ILE d 237 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU d 286 " --> pdb=" O VAL d 313 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASP d 315 " --> pdb=" O LEU d 286 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE d 288 " --> pdb=" O ASP d 315 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 196 through 200 removed outlier: 3.761A pdb=" N GLY D 381 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 213 through 214 removed outlier: 3.843A pdb=" N VAL D 363 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE D 360 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU D 351 " --> pdb=" O ARG D 362 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR D 364 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU D 349 " --> pdb=" O THR D 364 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 285 through 287 removed outlier: 6.196A pdb=" N LEU D 286 " --> pdb=" O VAL D 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 410 through 411 Processing sheet with id=AD6, first strand: chain 'e' and resid 72 through 75 removed outlier: 3.631A pdb=" N LYS e 72 " --> pdb=" O THR e 84 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR e 84 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR e 82 " --> pdb=" O LEU e 74 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'e' and resid 166 through 167 removed outlier: 3.632A pdb=" N ASP e 166 " --> pdb=" O VAL e 439 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'e' and resid 224 through 230 removed outlier: 6.492A pdb=" N LYS e 225 " --> pdb=" O CYS e 406 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL e 408 " --> pdb=" O LYS e 225 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN e 227 " --> pdb=" O VAL e 408 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLY e 410 " --> pdb=" O GLN e 227 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG e 229 " --> pdb=" O GLY e 410 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'e' and resid 342 through 343 removed outlier: 7.231A pdb=" N VAL e 321 " --> pdb=" O VAL e 343 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL e 320 " --> pdb=" O LYS e 268 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE e 322 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY e 375 " --> pdb=" O LEU e 269 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'e' and resid 381 through 382 removed outlier: 4.144A pdb=" N TYR e 381 " --> pdb=" O ILE e 394 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'e' and resid 551 through 554 removed outlier: 4.110A pdb=" N ILE e 551 " --> pdb=" O ASP h 50 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU h 52 " --> pdb=" O ILE e 551 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN e 553 " --> pdb=" O LEU h 52 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N VAL h 54 " --> pdb=" O ASN e 553 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE h 53 " --> pdb=" O THR h 61 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR h 61 " --> pdb=" O ILE h 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'E' and resid 166 through 167 Processing sheet with id=AE4, first strand: chain 'E' and resid 224 through 230 removed outlier: 6.252A pdb=" N LYS E 225 " --> pdb=" O CYS E 406 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL E 408 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLN E 227 " --> pdb=" O VAL E 408 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N GLY E 410 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG E 229 " --> pdb=" O GLY E 410 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 269 through 272 removed outlier: 6.152A pdb=" N ALA E 270 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL E 321 " --> pdb=" O VAL E 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 380 through 382 Processing sheet with id=AE7, first strand: chain 'E' and resid 554 through 556 removed outlier: 7.096A pdb=" N ILE E 555 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE H 51 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER H 63 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE H 53 " --> pdb=" O THR H 61 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR H 61 " --> pdb=" O ILE H 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'g' and resid 55 through 56 Processing sheet with id=AE9, first strand: chain 'g' and resid 141 through 142 Processing sheet with id=AF1, first strand: chain 'g' and resid 207 through 208 removed outlier: 3.790A pdb=" N GLU g 207 " --> pdb=" O ILE g 379 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU g 381 " --> pdb=" O GLU g 207 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'g' and resid 224 through 225 removed outlier: 3.729A pdb=" N LEU g 225 " --> pdb=" O SER g 366 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'g' and resid 294 through 296 Processing sheet with id=AF4, first strand: chain 'g' and resid 482 through 484 removed outlier: 3.675A pdb=" N VAL g 492 " --> pdb=" O GLY g 483 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 55 through 56 removed outlier: 4.201A pdb=" N VAL G 56 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU G 48 " --> pdb=" O VAL G 56 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AF7, first strand: chain 'G' and resid 206 through 208 Processing sheet with id=AF8, first strand: chain 'G' and resid 294 through 296 Processing sheet with id=AF9, first strand: chain 'G' and resid 482 through 484 Processing sheet with id=AG1, first strand: chain 'q' and resid 53 through 56 removed outlier: 4.010A pdb=" N LYS q 53 " --> pdb=" O THR q 65 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR q 65 " --> pdb=" O LYS q 53 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE q 55 " --> pdb=" O ILE q 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE q 63 " --> pdb=" O ILE q 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'q' and resid 207 through 213 removed outlier: 3.679A pdb=" N ILE q 212 " --> pdb=" O LEU q 386 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY q 388 " --> pdb=" O ILE q 212 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR q 383 " --> pdb=" O ILE q 223 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE q 223 " --> pdb=" O THR q 383 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'q' and resid 319 through 322 removed outlier: 7.500A pdb=" N GLU q 297 " --> pdb=" O LEU q 319 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU q 321 " --> pdb=" O GLU q 297 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE q 299 " --> pdb=" O LEU q 321 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS q 246 " --> pdb=" O VAL q 296 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N LEU q 341 " --> pdb=" O VAL q 247 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL q 249 " --> pdb=" O LEU q 341 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'q' and resid 319 through 322 removed outlier: 7.500A pdb=" N GLU q 297 " --> pdb=" O LEU q 319 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU q 321 " --> pdb=" O GLU q 297 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE q 299 " --> pdb=" O LEU q 321 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS q 246 " --> pdb=" O VAL q 296 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'q' and resid 360 through 362 Processing sheet with id=AG6, first strand: chain 'q' and resid 419 through 421 Processing sheet with id=AG7, first strand: chain 'q' and resid 544 through 545 removed outlier: 4.139A pdb=" N ILE q 545 " --> pdb=" O MET z 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'Q' and resid 62 through 63 removed outlier: 5.707A pdb=" N ILE Q 54 " --> pdb=" O ILE H 524 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 210 through 213 removed outlier: 3.749A pdb=" N VAL Q 210 " --> pdb=" O ILE Q 384 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU Q 386 " --> pdb=" O VAL Q 210 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE Q 212 " --> pdb=" O LEU Q 386 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY Q 388 " --> pdb=" O ILE Q 212 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 319 through 322 removed outlier: 3.523A pdb=" N LEU Q 321 " --> pdb=" O ILE Q 299 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS Q 246 " --> pdb=" O CYS Q 298 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL Q 300 " --> pdb=" O LYS Q 246 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA Q 248 " --> pdb=" O VAL Q 300 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N LEU Q 341 " --> pdb=" O VAL Q 247 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL Q 249 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 319 through 322 removed outlier: 3.523A pdb=" N LEU Q 321 " --> pdb=" O ILE Q 299 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS Q 246 " --> pdb=" O CYS Q 298 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL Q 300 " --> pdb=" O LYS Q 246 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA Q 248 " --> pdb=" O VAL Q 300 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 357 through 363 removed outlier: 3.847A pdb=" N THR Q 357 " --> pdb=" O LYS Q 372 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS Q 372 " --> pdb=" O THR Q 357 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS Q 359 " --> pdb=" O VAL Q 370 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP Q 366 " --> pdb=" O ILE Q 363 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 419 through 421 Processing sheet with id=AH5, first strand: chain 'Q' and resid 544 through 545 removed outlier: 6.239A pdb=" N ILE Q 545 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS Z 54 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'z' and resid 138 through 139 Processing sheet with id=AH7, first strand: chain 'z' and resid 195 through 199 removed outlier: 6.416A pdb=" N GLU z 195 " --> pdb=" O ILE z 378 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE z 380 " --> pdb=" O GLU z 195 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET z 197 " --> pdb=" O ILE z 380 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'z' and resid 227 through 228 Processing sheet with id=AH9, first strand: chain 'z' and resid 231 through 234 removed outlier: 5.882A pdb=" N TYR z 232 " --> pdb=" O VAL z 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'z' and resid 490 through 491 Processing sheet with id=AI2, first strand: chain 'Z' and resid 138 through 139 Processing sheet with id=AI3, first strand: chain 'Z' and resid 194 through 197 removed outlier: 6.116A pdb=" N GLU Z 195 " --> pdb=" O ILE Z 378 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Z' and resid 227 through 228 Processing sheet with id=AI5, first strand: chain 'Z' and resid 292 through 295 removed outlier: 6.033A pdb=" N TYR Z 232 " --> pdb=" O VAL Z 294 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N GLN Z 337 " --> pdb=" O VAL Z 233 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE Z 235 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'Z' and resid 490 through 491 Processing sheet with id=AI7, first strand: chain 'h' and resid 145 through 146 removed outlier: 3.580A pdb=" N VAL h 145 " --> pdb=" O ILE h 409 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE h 409 " --> pdb=" O VAL h 145 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'h' and resid 199 through 200 removed outlier: 5.831A pdb=" N GLY h 200 " --> pdb=" O LEU h 376 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'h' and resid 203 through 205 removed outlier: 6.405A pdb=" N ILE h 204 " --> pdb=" O GLY h 380 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI9 Processing sheet with id=AJ1, first strand: chain 'h' and resid 235 through 236 removed outlier: 4.142A pdb=" N PHE h 352 " --> pdb=" O PHE h 236 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'h' and resid 313 through 315 removed outlier: 3.562A pdb=" N ALA h 315 " --> pdb=" O VAL h 293 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS h 240 " --> pdb=" O ILE h 292 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU h 294 " --> pdb=" O LYS h 240 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU h 242 " --> pdb=" O LEU h 294 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N GLN h 335 " --> pdb=" O ILE h 241 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER h 243 " --> pdb=" O GLN h 335 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'h' and resid 313 through 315 removed outlier: 3.562A pdb=" N ALA h 315 " --> pdb=" O VAL h 293 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS h 240 " --> pdb=" O ILE h 292 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU h 294 " --> pdb=" O LYS h 240 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU h 242 " --> pdb=" O LEU h 294 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'h' and resid 479 through 481 removed outlier: 3.923A pdb=" N GLY h 489 " --> pdb=" O GLY h 480 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'H' and resid 145 through 146 removed outlier: 3.754A pdb=" N VAL H 145 " --> pdb=" O ILE H 409 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE H 409 " --> pdb=" O VAL H 145 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'H' and resid 199 through 204 removed outlier: 6.532A pdb=" N GLY H 200 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU H 378 " --> pdb=" O GLY H 200 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS H 202 " --> pdb=" O LEU H 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR H 375 " --> pdb=" O ILE H 215 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'H' and resid 241 through 244 removed outlier: 3.674A pdb=" N LEU H 294 " --> pdb=" O LEU H 242 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'H' and resid 351 through 355 removed outlier: 3.603A pdb=" N GLU H 353 " --> pdb=" O LEU H 364 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'H' and resid 479 through 481 removed outlier: 3.810A pdb=" N GLY H 489 " --> pdb=" O GLY H 480 " (cutoff:3.500A) 2424 hydrogen bonds defined for protein. 7026 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: 19.30 Time building geometry restraints manager: 18.71 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: 20646 1.34 - 1.46: 11267 1.46 - 1.58: 29254 1.58 - 1.70: 0 1.70 - 1.81: 504 Bond restraints: 61671 Sorted by residual: bond pdb=" C ARG d 372 " pdb=" N PRO d 373 " ideal model delta sigma weight residual 1.334 1.441 -0.107 2.34e-02 1.83e+03 2.09e+01 bond pdb=" C ALA q 346 " pdb=" N PRO q 347 " ideal model delta sigma weight residual 1.334 1.425 -0.091 2.34e-02 1.83e+03 1.51e+01 bond pdb=" C ALA Q 346 " pdb=" N PRO Q 347 " ideal model delta sigma weight residual 1.334 1.407 -0.073 2.34e-02 1.83e+03 9.77e+00 bond pdb=" C SER G 409 " pdb=" N PRO G 410 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.43e+00 bond pdb=" CA ILE E 479 " pdb=" CB ILE E 479 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 2.30e+00 ... (remaining 61666 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.29: 1399 107.29 - 113.97: 36861 113.97 - 120.64: 24827 120.64 - 127.31: 19720 127.31 - 133.98: 376 Bond angle restraints: 83183 Sorted by residual: angle pdb=" N GLY h 228 " pdb=" CA GLY h 228 " pdb=" C GLY h 228 " ideal model delta sigma weight residual 116.01 121.21 -5.20 1.64e+00 3.72e-01 1.00e+01 angle pdb=" N HIS e 353 " pdb=" CA HIS e 353 " pdb=" C HIS e 353 " ideal model delta sigma weight residual 110.80 117.05 -6.25 2.13e+00 2.20e-01 8.61e+00 angle pdb=" C PHE H 229 " pdb=" N GLU H 230 " pdb=" CA GLU H 230 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.63e+00 angle pdb=" C ILE e 244 " pdb=" N LEU e 245 " pdb=" CA LEU e 245 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.15e+00 angle pdb=" C GLY B 466 " pdb=" N ILE B 467 " pdb=" CA ILE B 467 " ideal model delta sigma weight residual 121.97 126.74 -4.77 1.80e+00 3.09e-01 7.02e+00 ... (remaining 83178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 37702 15.98 - 31.96: 322 31.96 - 47.94: 190 47.94 - 63.91: 57 63.91 - 79.89: 6 Dihedral angle restraints: 38277 sinusoidal: 15299 harmonic: 22978 Sorted by residual: dihedral pdb=" CA ASP z 16 " pdb=" C ASP z 16 " pdb=" N ALA z 17 " pdb=" CA ALA z 17 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ASP H 272 " pdb=" C ASP H 272 " pdb=" N ALA H 273 " pdb=" CA ALA H 273 " ideal model delta harmonic sigma weight residual -180.00 -153.54 -26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA VAL H 271 " pdb=" C VAL H 271 " pdb=" N ASP H 272 " pdb=" CA ASP H 272 " ideal model delta harmonic sigma weight residual -180.00 -154.82 -25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 38274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 7332 0.038 - 0.075: 1925 0.075 - 0.113: 640 0.113 - 0.150: 119 0.150 - 0.188: 2 Chirality restraints: 10018 Sorted by residual: chirality pdb=" CA GLU h 230 " pdb=" N GLU h 230 " pdb=" C GLU h 230 " pdb=" CB GLU h 230 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CB ILE e 244 " pdb=" CA ILE e 244 " pdb=" CG1 ILE e 244 " pdb=" CG2 ILE e 244 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA HIS e 353 " pdb=" N HIS e 353 " pdb=" C HIS e 353 " pdb=" CB HIS e 353 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 10015 not shown) Planarity restraints: 10682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 372 " -0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO D 373 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 373 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 373 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS e 280 " 0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO e 281 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO e 281 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO e 281 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 278 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO E 279 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 279 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 279 " 0.022 5.00e-02 4.00e+02 ... (remaining 10679 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 9385 2.76 - 3.30: 57069 3.30 - 3.83: 90633 3.83 - 4.37: 107636 4.37 - 4.90: 185213 Nonbonded interactions: 449936 Sorted by model distance: nonbonded pdb=" O LEU E 223 " pdb=" OG1 THR E 403 " model vdw 2.226 2.440 nonbonded pdb=" O LEU H 198 " pdb=" OG1 THR H 373 " model vdw 2.253 2.440 nonbonded pdb=" OH TYR Z 182 " pdb=" O GLN Z 185 " model vdw 2.260 2.440 nonbonded pdb=" O VAL Z 367 " pdb=" ND2 ASN Z 370 " model vdw 2.265 2.520 nonbonded pdb=" O LEU h 198 " pdb=" OG1 THR h 373 " model vdw 2.269 2.440 ... (remaining 449931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 256 or resid 276 through 547)) selection = chain 'a' } ncs_group { reference = (chain 'B' and resid 19 through 520) selection = chain 'b' } ncs_group { reference = (chain 'D' and (resid 17 through 479 or resid 492 through 528)) selection = (chain 'd' and (resid 17 through 233 or resid 282 through 289 or resid 298 throu \ gh 328 or resid 347 through 528)) } ncs_group { reference = (chain 'E' and resid 42 through 560) selection = (chain 'e' and (resid 42 through 281 or resid 308 through 560)) } ncs_group { reference = (chain 'G' and resid 17 through 530) selection = (chain 'g' and (resid 17 through 246 or resid 290 through 335 or resid 349 throu \ gh 530)) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'Q' selection = (chain 'q' and resid 27 through 549) } ncs_group { reference = (chain 'Z' and (resid 8 through 254 or resid 262 through 538)) selection = chain 'z' } 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: 0.300 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: 0.030 Extract box with map and model: 4.450 Check model and map are aligned: 0.680 Set scattering table: 0.420 Process input model: 115.760 Find NCS groups from input model: 5.210 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5251 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 : 0.001 0.107 61671 Z= 0.088 Angle : 0.390 8.276 83183 Z= 0.221 Chirality : 0.039 0.188 10018 Planarity : 0.002 0.058 10682 Dihedral : 7.152 79.892 23381 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.46 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.07), residues: 7946 helix: -3.61 (0.05), residues: 3509 sheet: -0.90 (0.20), residues: 483 loop : -1.19 (0.08), residues: 3954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.000 TRP h 275 HIS 0.006 0.000 HIS e 353 PHE 0.025 0.001 PHE E 276 TYR 0.007 0.000 TYR G 442 ARG 0.003 0.000 ARG a 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2378 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2378 time to evaluate : 5.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 107 GLU cc_start: 0.8467 (tp30) cc_final: 0.8192 (tp30) REVERT: a 115 LEU cc_start: 0.7865 (mt) cc_final: 0.7352 (tt) REVERT: a 316 MET cc_start: 0.0467 (mtp) cc_final: -0.0709 (tpp) REVERT: a 402 LEU cc_start: 0.2972 (tp) cc_final: 0.2317 (tt) REVERT: a 420 PRO cc_start: 0.6358 (Cg_endo) cc_final: 0.6093 (Cg_exo) REVERT: a 493 LYS cc_start: 0.5395 (pttt) cc_final: 0.4802 (mtmm) REVERT: a 502 LEU cc_start: 0.7197 (mt) cc_final: 0.6669 (mt) REVERT: a 522 ILE cc_start: 0.8391 (mt) cc_final: 0.8190 (mm) REVERT: A 27 ASN cc_start: 0.7889 (m-40) cc_final: 0.7294 (p0) REVERT: A 54 VAL cc_start: 0.5390 (t) cc_final: 0.5183 (t) REVERT: A 101 VAL cc_start: 0.9486 (t) cc_final: 0.9073 (t) REVERT: A 111 ARG cc_start: 0.8270 (mtt-85) cc_final: 0.7971 (mmt90) REVERT: A 156 LEU cc_start: 0.7098 (mt) cc_final: 0.6795 (tp) REVERT: A 448 ILE cc_start: 0.8794 (mt) cc_final: 0.8441 (tp) REVERT: A 530 SER cc_start: 0.7611 (m) cc_final: 0.6101 (t) REVERT: A 542 ASP cc_start: 0.6908 (m-30) cc_final: 0.5067 (m-30) REVERT: A 544 MET cc_start: 0.4783 (ttt) cc_final: 0.4552 (ttt) REVERT: b 121 ILE cc_start: 0.6831 (mt) cc_final: 0.6548 (mm) REVERT: b 451 ASP cc_start: 0.6931 (t0) cc_final: 0.6675 (t0) REVERT: b 474 LEU cc_start: 0.7355 (mt) cc_final: 0.7096 (mt) REVERT: B 27 ILE cc_start: 0.7044 (mt) cc_final: 0.6533 (tt) REVERT: B 263 LYS cc_start: 0.7472 (mttt) cc_final: 0.7068 (tptt) REVERT: B 397 GLU cc_start: 0.5813 (tt0) cc_final: 0.4983 (pt0) REVERT: B 413 LYS cc_start: 0.8457 (pttt) cc_final: 0.7991 (mmtp) REVERT: B 447 ASN cc_start: 0.7986 (m-40) cc_final: 0.7610 (m-40) REVERT: B 455 LEU cc_start: 0.8231 (mt) cc_final: 0.7788 (mm) REVERT: d 37 THR cc_start: 0.8765 (p) cc_final: 0.8464 (t) REVERT: d 116 HIS cc_start: 0.7499 (t-90) cc_final: 0.6758 (t-90) REVERT: d 129 LYS cc_start: 0.7960 (mttt) cc_final: 0.7713 (ptmt) REVERT: d 210 ILE cc_start: 0.7687 (mm) cc_final: 0.7485 (mt) REVERT: d 402 ARG cc_start: 0.5808 (ttp80) cc_final: 0.5567 (tpt90) REVERT: d 457 ASN cc_start: 0.8173 (m-40) cc_final: 0.7884 (m-40) REVERT: d 513 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7068 (mm-30) REVERT: D 48 ILE cc_start: 0.4498 (mt) cc_final: 0.4066 (mt) REVERT: D 155 SER cc_start: 0.7836 (t) cc_final: 0.7481 (p) REVERT: D 440 TRP cc_start: 0.7256 (m100) cc_final: 0.6911 (m-10) REVERT: e 158 ILE cc_start: 0.7796 (mt) cc_final: 0.7484 (mm) REVERT: e 428 CYS cc_start: 0.6543 (m) cc_final: 0.4941 (m) REVERT: e 535 LYS cc_start: 0.8188 (tttt) cc_final: 0.7561 (mmtm) REVERT: E 175 LEU cc_start: 0.7641 (tp) cc_final: 0.7161 (tp) REVERT: E 212 MET cc_start: 0.6706 (ttp) cc_final: 0.6264 (ttp) REVERT: E 406 CYS cc_start: 0.5390 (m) cc_final: 0.5045 (m) REVERT: g 103 ILE cc_start: 0.8368 (mt) cc_final: 0.8038 (mm) REVERT: g 365 PHE cc_start: -0.0299 (m-10) cc_final: -0.0647 (m-10) REVERT: g 387 ASP cc_start: 0.4198 (m-30) cc_final: 0.3656 (t70) REVERT: g 413 SER cc_start: 0.8639 (m) cc_final: 0.7984 (t) REVERT: g 420 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7300 (tp30) REVERT: g 514 ILE cc_start: 0.9171 (mm) cc_final: 0.8781 (mm) REVERT: G 183 ARG cc_start: 0.6184 (ptt90) cc_final: 0.5800 (tmm-80) REVERT: G 298 GLU cc_start: 0.6269 (tt0) cc_final: 0.5982 (tm-30) REVERT: G 367 PHE cc_start: 0.1787 (m-10) cc_final: 0.1484 (m-10) REVERT: G 408 LEU cc_start: 0.7849 (mt) cc_final: 0.7168 (tt) REVERT: q 83 LYS cc_start: 0.8149 (mttt) cc_final: 0.7743 (mtpp) REVERT: q 154 ASN cc_start: 0.4836 (m-40) cc_final: 0.4244 (t0) REVERT: q 161 LYS cc_start: 0.9273 (mttt) cc_final: 0.8984 (mttm) REVERT: q 403 ASP cc_start: 0.6727 (m-30) cc_final: 0.6460 (m-30) REVERT: q 445 LEU cc_start: 0.7901 (mt) cc_final: 0.7343 (mt) REVERT: q 484 VAL cc_start: 0.5064 (m) cc_final: 0.3603 (t) REVERT: q 525 LYS cc_start: 0.8220 (tttt) cc_final: 0.7781 (ttmt) REVERT: Q 216 SER cc_start: 0.4310 (t) cc_final: 0.4084 (m) REVERT: Q 313 LEU cc_start: 0.5353 (mt) cc_final: 0.4894 (mt) REVERT: Q 530 VAL cc_start: 0.9535 (t) cc_final: 0.9326 (p) REVERT: z 43 LEU cc_start: 0.8119 (tp) cc_final: 0.7872 (tp) REVERT: z 106 HIS cc_start: 0.7490 (t-90) cc_final: 0.7264 (t-90) REVERT: z 215 LEU cc_start: 0.7449 (pp) cc_final: 0.7141 (mp) REVERT: Z 43 LEU cc_start: 0.7049 (tp) cc_final: 0.6753 (tt) REVERT: h 30 ILE cc_start: 0.9292 (mt) cc_final: 0.9080 (mm) REVERT: h 103 ILE cc_start: 0.9023 (mt) cc_final: 0.8631 (mt) REVERT: h 109 MET cc_start: 0.7941 (mtm) cc_final: 0.7274 (mpp) REVERT: h 253 GLU cc_start: -0.0241 (mt-10) cc_final: -0.0565 (tt0) REVERT: h 268 GLN cc_start: 0.3957 (mm110) cc_final: 0.3665 (pt0) REVERT: h 272 ASP cc_start: 0.1252 (m-30) cc_final: 0.0715 (m-30) REVERT: h 417 GLU cc_start: 0.8257 (tp30) cc_final: 0.7728 (tp30) REVERT: h 423 CYS cc_start: 0.5774 (m) cc_final: 0.5169 (m) REVERT: h 427 TYR cc_start: 0.6167 (m-10) cc_final: 0.5344 (m-80) REVERT: h 515 ASN cc_start: 0.8088 (m-40) cc_final: 0.7518 (t0) REVERT: H 37 GLN cc_start: 0.8530 (tt0) cc_final: 0.7792 (pp30) REVERT: H 108 LEU cc_start: 0.7657 (mt) cc_final: 0.7433 (mt) REVERT: H 126 MET cc_start: 0.7534 (mtm) cc_final: 0.7296 (mtm) REVERT: H 249 GLU cc_start: 0.1132 (pm20) cc_final: -0.1281 (tp30) REVERT: H 292 ILE cc_start: 0.3601 (mm) cc_final: 0.3294 (mm) REVERT: H 323 MET cc_start: 0.6333 (mmm) cc_final: 0.6017 (ppp) REVERT: H 404 LEU cc_start: 0.5963 (mt) cc_final: 0.5732 (mt) REVERT: H 462 ILE cc_start: 0.6497 (mt) cc_final: 0.5937 (mt) REVERT: H 496 VAL cc_start: 0.7307 (t) cc_final: 0.6587 (t) REVERT: H 515 ASN cc_start: 0.7899 (m-40) cc_final: 0.7402 (m-40) outliers start: 0 outliers final: 0 residues processed: 2378 average time/residue: 0.6232 time to fit residues: 2445.6116 Evaluate side-chains 1252 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1252 time to evaluate : 5.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 671 optimal weight: 10.0000 chunk 602 optimal weight: 6.9990 chunk 334 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 406 optimal weight: 10.0000 chunk 321 optimal weight: 6.9990 chunk 623 optimal weight: 9.9990 chunk 241 optimal weight: 0.6980 chunk 378 optimal weight: 1.9990 chunk 463 optimal weight: 4.9990 chunk 721 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 38 ASN a 88 GLN a 89 GLN ** a 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 HIS a 430 ASN ** a 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 514 HIS A 77 HIS ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS A 485 GLN b 142 ASN b 155 HIS b 222 GLN b 286 ASN ** b 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS d 149 GLN ** d 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 289 GLN d 395 HIS ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN D 289 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 ASN e 337 GLN e 349 GLN e 397 GLN e 474 GLN e 502 GLN e 536 GLN E 353 HIS ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 123 GLN g 397 GLN ** g 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 GLN q 391 GLN q 482 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 ASN Q 79 HIS ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 GLN Q 446 GLN ** z 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 329 GLN z 356 GLN Z 185 GLN Z 329 GLN Z 337 GLN Z 356 GLN Z 430 ASN ** h 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 172 HIS ** h 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 HIS H 216 ASN H 231 GLN H 405 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 61671 Z= 0.229 Angle : 0.623 11.648 83183 Z= 0.327 Chirality : 0.045 0.298 10018 Planarity : 0.004 0.157 10682 Dihedral : 3.645 25.947 8441 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.52 % Rotamer: Outliers : 0.10 % Allowed : 2.64 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.08), residues: 7946 helix: -0.96 (0.08), residues: 3641 sheet: -0.48 (0.19), residues: 605 loop : -0.98 (0.09), residues: 3700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 167 HIS 0.015 0.001 HIS d 62 PHE 0.022 0.002 PHE B 218 TYR 0.019 0.002 TYR b 124 ARG 0.017 0.001 ARG e 431 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1673 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1666 time to evaluate : 5.197 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: a 38 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8921 (t0) REVERT: a 125 ILE cc_start: 0.9688 (mm) cc_final: 0.9373 (tp) REVERT: a 233 MET cc_start: -0.0196 (mtp) cc_final: -0.0409 (mtp) REVERT: a 244 ILE cc_start: 0.7432 (mt) cc_final: 0.7205 (mt) REVERT: a 316 MET cc_start: 0.2790 (mtp) cc_final: 0.1386 (tpt) REVERT: a 348 GLU cc_start: 0.7060 (pt0) cc_final: 0.6795 (pt0) REVERT: a 402 LEU cc_start: 0.2827 (tp) cc_final: 0.2505 (tt) REVERT: a 429 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8344 (tt) REVERT: a 471 SER cc_start: 0.9474 (m) cc_final: 0.9238 (t) REVERT: a 472 GLU cc_start: 0.8432 (tp30) cc_final: 0.8111 (tp30) REVERT: A 27 ASN cc_start: 0.8188 (m-40) cc_final: 0.7616 (m-40) REVERT: A 49 LEU cc_start: 0.4136 (mt) cc_final: 0.3494 (mt) REVERT: A 88 GLN cc_start: 0.7484 (mm-40) cc_final: 0.6990 (mm110) REVERT: A 107 GLU cc_start: 0.8228 (tp30) cc_final: 0.7751 (tp30) REVERT: A 111 ARG cc_start: 0.8613 (mtt-85) cc_final: 0.8121 (mmt90) REVERT: A 156 LEU cc_start: 0.7313 (mt) cc_final: 0.7067 (mm) REVERT: A 219 VAL cc_start: 0.3864 (p) cc_final: 0.3623 (p) REVERT: A 233 MET cc_start: 0.4162 (tpp) cc_final: 0.3509 (tpp) REVERT: A 446 LEU cc_start: 0.8712 (mt) cc_final: 0.8496 (mt) REVERT: A 450 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7740 (tt0) REVERT: b 87 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7055 (mt-10) REVERT: b 98 LEU cc_start: 0.8570 (tp) cc_final: 0.8254 (tt) REVERT: b 347 MET cc_start: 0.4667 (mpp) cc_final: 0.4463 (mpp) REVERT: B 27 ILE cc_start: 0.7163 (mt) cc_final: 0.6661 (tt) REVERT: B 42 MET cc_start: 0.7250 (tpt) cc_final: 0.6989 (tpt) REVERT: B 263 LYS cc_start: 0.7628 (mttt) cc_final: 0.7158 (tptt) REVERT: B 413 LYS cc_start: 0.8384 (pttt) cc_final: 0.7858 (mptt) REVERT: B 451 ASP cc_start: 0.7341 (t0) cc_final: 0.7045 (t0) REVERT: B 512 ASP cc_start: 0.6306 (p0) cc_final: 0.5414 (p0) REVERT: d 30 SER cc_start: 0.8671 (m) cc_final: 0.8171 (t) REVERT: d 36 ARG cc_start: 0.7928 (ttp-110) cc_final: 0.7233 (ptt-90) REVERT: d 190 ASP cc_start: 0.5097 (t70) cc_final: 0.4800 (t70) REVERT: d 410 LEU cc_start: 0.7489 (mp) cc_final: 0.7271 (mt) REVERT: d 436 GLN cc_start: 0.8473 (pp30) cc_final: 0.7696 (pp30) REVERT: d 438 PHE cc_start: 0.7468 (t80) cc_final: 0.6568 (t80) REVERT: d 457 ASN cc_start: 0.8389 (m-40) cc_final: 0.7943 (m110) REVERT: D 66 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7739 (mtpt) REVERT: D 155 SER cc_start: 0.7657 (t) cc_final: 0.6955 (p) REVERT: D 440 TRP cc_start: 0.7011 (m100) cc_final: 0.6517 (m-10) REVERT: D 441 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8121 (mm-40) REVERT: e 55 ARG cc_start: 0.7459 (mmm-85) cc_final: 0.7202 (mmm-85) REVERT: e 452 LEU cc_start: 0.9049 (pp) cc_final: 0.8774 (tt) REVERT: E 176 PHE cc_start: 0.5766 (t80) cc_final: 0.5444 (t80) REVERT: E 210 ASN cc_start: 0.5683 (m-40) cc_final: 0.5271 (m-40) REVERT: E 212 MET cc_start: 0.6630 (ttp) cc_final: 0.6047 (ttp) REVERT: E 225 LYS cc_start: 0.2860 (tttt) cc_final: 0.2629 (mtpt) REVERT: E 495 LEU cc_start: 0.9140 (tp) cc_final: 0.8728 (tp) REVERT: g 122 ILE cc_start: 0.9212 (mt) cc_final: 0.8870 (mt) REVERT: g 171 MET cc_start: 0.5265 (mmp) cc_final: 0.4894 (mmm) REVERT: g 425 VAL cc_start: 0.8877 (t) cc_final: 0.8598 (p) REVERT: g 518 CYS cc_start: 0.8891 (p) cc_final: 0.7772 (t) REVERT: G 144 ASP cc_start: 0.5265 (p0) cc_final: 0.4481 (p0) REVERT: G 455 THR cc_start: 0.8635 (t) cc_final: 0.8069 (p) REVERT: G 459 ASN cc_start: 0.8198 (m-40) cc_final: 0.7570 (m-40) REVERT: q 41 MET cc_start: 0.5477 (tmm) cc_final: 0.4916 (tmm) REVERT: q 132 ASN cc_start: 0.8514 (m-40) cc_final: 0.8287 (m-40) REVERT: q 154 ASN cc_start: 0.5883 (m-40) cc_final: 0.4871 (t0) REVERT: q 161 LYS cc_start: 0.9353 (mttt) cc_final: 0.9015 (mttm) REVERT: q 179 SER cc_start: 0.7061 (p) cc_final: 0.6590 (t) REVERT: q 449 ILE cc_start: 0.9053 (mm) cc_final: 0.8753 (mm) REVERT: q 511 ASP cc_start: 0.7833 (t0) cc_final: 0.7446 (t0) REVERT: Q 83 LYS cc_start: 0.7320 (mtmt) cc_final: 0.6309 (tttp) REVERT: Q 92 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7022 (mm-40) REVERT: Q 431 ILE cc_start: 0.8432 (mm) cc_final: 0.8209 (mm) REVERT: Q 528 ILE cc_start: 0.8717 (mm) cc_final: 0.8271 (mm) REVERT: Q 530 VAL cc_start: 0.9425 (t) cc_final: 0.9188 (p) REVERT: z 224 MET cc_start: 0.2404 (mmp) cc_final: -0.0689 (mtm) REVERT: z 380 ILE cc_start: 0.7172 (mt) cc_final: 0.6966 (mt) REVERT: z 422 LEU cc_start: 0.9369 (tp) cc_final: 0.8945 (tt) REVERT: z 434 LEU cc_start: 0.5650 (mt) cc_final: 0.5435 (mt) REVERT: Z 36 ASN cc_start: 0.8708 (p0) cc_final: 0.8461 (p0) REVERT: Z 43 LEU cc_start: 0.7321 (tp) cc_final: 0.6961 (tt) REVERT: Z 46 LEU cc_start: 0.8007 (mt) cc_final: 0.7767 (mt) REVERT: Z 57 LYS cc_start: 0.6767 (mtpp) cc_final: 0.5823 (ttpp) REVERT: Z 114 HIS cc_start: 0.8267 (t-90) cc_final: 0.7968 (t-90) REVERT: Z 193 MET cc_start: 0.6913 (ppp) cc_final: 0.6272 (tmm) REVERT: Z 287 MET cc_start: 0.4280 (tpt) cc_final: 0.3778 (tpt) REVERT: h 268 GLN cc_start: 0.3745 (mm110) cc_final: 0.3399 (pt0) REVERT: h 355 MET cc_start: 0.4069 (ppp) cc_final: 0.3389 (tpp) REVERT: h 427 TYR cc_start: 0.6488 (m-10) cc_final: 0.6048 (m-80) REVERT: h 456 ASN cc_start: 0.8169 (m-40) cc_final: 0.7722 (m-40) REVERT: h 476 GLU cc_start: 0.4955 (mp0) cc_final: 0.4179 (mp0) REVERT: h 477 LYS cc_start: 0.8124 (pttm) cc_final: 0.7764 (pttm) REVERT: H 37 GLN cc_start: 0.8911 (tt0) cc_final: 0.8372 (pp30) REVERT: H 107 GLU cc_start: 0.8169 (tp30) cc_final: 0.7907 (tp30) REVERT: H 108 LEU cc_start: 0.8037 (mt) cc_final: 0.7821 (mp) REVERT: H 126 MET cc_start: 0.7730 (mtm) cc_final: 0.7450 (mtm) REVERT: H 166 MET cc_start: 0.4324 (mmt) cc_final: 0.3995 (mmt) REVERT: H 292 ILE cc_start: 0.3702 (mm) cc_final: 0.3406 (mm) REVERT: H 416 THR cc_start: 0.7251 (p) cc_final: 0.7007 (p) REVERT: H 419 GLU cc_start: 0.5305 (mp0) cc_final: 0.5056 (mp0) REVERT: H 438 ILE cc_start: 0.8583 (mt) cc_final: 0.8349 (mt) REVERT: H 444 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8176 (tmtt) REVERT: H 460 ASP cc_start: 0.7098 (t0) cc_final: 0.6672 (t0) REVERT: H 467 LYS cc_start: 0.7998 (ttpt) cc_final: 0.7687 (ttpt) REVERT: H 490 ASP cc_start: 0.7323 (t0) cc_final: 0.6836 (t0) REVERT: H 504 ILE cc_start: 0.8675 (mt) cc_final: 0.8362 (mt) REVERT: H 515 ASN cc_start: 0.8398 (m-40) cc_final: 0.7278 (m-40) REVERT: H 521 ASP cc_start: 0.7484 (p0) cc_final: 0.7264 (p0) outliers start: 7 outliers final: 1 residues processed: 1668 average time/residue: 0.5458 time to fit residues: 1552.0958 Evaluate side-chains 1187 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1184 time to evaluate : 5.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 401 optimal weight: 7.9990 chunk 224 optimal weight: 20.0000 chunk 600 optimal weight: 7.9990 chunk 491 optimal weight: 0.0270 chunk 199 optimal weight: 5.9990 chunk 723 optimal weight: 7.9990 chunk 781 optimal weight: 5.9990 chunk 644 optimal weight: 0.0770 chunk 717 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 580 optimal weight: 2.9990 overall best weight: 2.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 499 ASN a 514 HIS ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 395 HIS ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 496 HIS ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 HIS D 499 GLN ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 HIS g 443 GLN ** g 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 GLN G 475 HIS ** q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 ASN q 451 GLN ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 22 ASN ** z 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 430 ASN ** Z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 GLN ** h 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 472 HIS ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 505 ASN H 90 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 61671 Z= 0.211 Angle : 0.593 14.356 83183 Z= 0.305 Chirality : 0.044 0.216 10018 Planarity : 0.004 0.072 10682 Dihedral : 3.880 27.321 8441 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Rotamer: Outliers : 0.10 % Allowed : 2.33 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.09), residues: 7946 helix: -0.11 (0.08), residues: 3708 sheet: -0.31 (0.20), residues: 602 loop : -0.88 (0.09), residues: 3636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP g 167 HIS 0.015 0.001 HIS E 50 PHE 0.041 0.002 PHE e 249 TYR 0.017 0.002 TYR H 479 ARG 0.010 0.001 ARG D 520 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1524 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1517 time to evaluate : 5.264 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 125 ILE cc_start: 0.9703 (mm) cc_final: 0.9497 (tp) REVERT: a 316 MET cc_start: 0.2061 (mtp) cc_final: 0.1482 (tpt) REVERT: a 471 SER cc_start: 0.9456 (m) cc_final: 0.9093 (t) REVERT: a 545 ILE cc_start: 0.8157 (mt) cc_final: 0.7773 (mp) REVERT: A 27 ASN cc_start: 0.8194 (m-40) cc_final: 0.7656 (m-40) REVERT: A 107 GLU cc_start: 0.8245 (tp30) cc_final: 0.8032 (tp30) REVERT: A 179 MET cc_start: 0.5869 (mmm) cc_final: 0.5512 (mmp) REVERT: A 219 VAL cc_start: 0.3409 (p) cc_final: 0.3147 (p) REVERT: A 233 MET cc_start: 0.4380 (tpp) cc_final: 0.3768 (tpp) REVERT: A 398 MET cc_start: 0.5568 (mmp) cc_final: 0.5045 (tpp) REVERT: A 532 LEU cc_start: 0.9159 (mp) cc_final: 0.8496 (tt) REVERT: b 31 ASP cc_start: 0.7355 (m-30) cc_final: 0.6952 (m-30) REVERT: b 36 THR cc_start: 0.8997 (p) cc_final: 0.8541 (t) REVERT: b 98 LEU cc_start: 0.8842 (tp) cc_final: 0.8472 (tt) REVERT: b 347 MET cc_start: 0.5455 (mpp) cc_final: 0.5204 (mpp) REVERT: B 27 ILE cc_start: 0.7411 (mt) cc_final: 0.7146 (tt) REVERT: B 31 ASP cc_start: 0.7910 (p0) cc_final: 0.7617 (p0) REVERT: B 137 LYS cc_start: 0.7067 (mttt) cc_final: 0.6598 (tmtt) REVERT: B 263 LYS cc_start: 0.7572 (mttt) cc_final: 0.6896 (tptp) REVERT: B 413 LYS cc_start: 0.8544 (pttt) cc_final: 0.7873 (mmtt) REVERT: B 431 GLU cc_start: 0.7553 (tm-30) cc_final: 0.6147 (tm-30) REVERT: B 435 ARG cc_start: 0.7705 (mtm180) cc_final: 0.7122 (mtm180) REVERT: B 451 ASP cc_start: 0.7450 (t0) cc_final: 0.7125 (t0) REVERT: d 30 SER cc_start: 0.8887 (m) cc_final: 0.8347 (t) REVERT: d 47 MET cc_start: 0.6952 (tmm) cc_final: 0.6465 (tmm) REVERT: d 118 THR cc_start: 0.8751 (m) cc_final: 0.8549 (m) REVERT: d 152 ARG cc_start: 0.6109 (ttm170) cc_final: 0.5769 (mtp180) REVERT: d 192 ASN cc_start: 0.5932 (m-40) cc_final: 0.5697 (t0) REVERT: d 436 GLN cc_start: 0.8542 (pp30) cc_final: 0.8212 (pp30) REVERT: d 502 LEU cc_start: 0.8863 (tp) cc_final: 0.8625 (tp) REVERT: D 132 VAL cc_start: 0.8915 (t) cc_final: 0.8631 (t) REVERT: D 138 MET cc_start: 0.7387 (mtt) cc_final: 0.7169 (mtt) REVERT: D 155 SER cc_start: 0.7630 (t) cc_final: 0.6966 (p) REVERT: D 441 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8171 (mm-40) REVERT: D 461 ASN cc_start: 0.8926 (t0) cc_final: 0.8717 (t0) REVERT: D 477 GLU cc_start: 0.5039 (pp20) cc_final: 0.4716 (pp20) REVERT: e 142 HIS cc_start: 0.7941 (t70) cc_final: 0.7713 (t70) REVERT: e 145 LYS cc_start: 0.8352 (mmmm) cc_final: 0.8102 (mmtt) REVERT: e 146 ILE cc_start: 0.9222 (mt) cc_final: 0.8954 (mt) REVERT: e 452 LEU cc_start: 0.9090 (pp) cc_final: 0.8840 (tt) REVERT: e 474 GLN cc_start: 0.8160 (tp40) cc_final: 0.7707 (tp40) REVERT: E 112 ASP cc_start: 0.7044 (p0) cc_final: 0.6706 (p0) REVERT: E 212 MET cc_start: 0.6359 (ttp) cc_final: 0.5825 (ttp) REVERT: E 495 LEU cc_start: 0.8978 (tp) cc_final: 0.8564 (tp) REVERT: g 102 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8631 (mm-30) REVERT: g 106 GLN cc_start: 0.7080 (tp-100) cc_final: 0.6745 (tp-100) REVERT: g 234 MET cc_start: 0.1294 (mmm) cc_final: 0.0799 (mmm) REVERT: G 18 ARG cc_start: 0.6427 (tpp-160) cc_final: 0.6069 (tpp-160) REVERT: G 151 MET cc_start: 0.7646 (mpp) cc_final: 0.7323 (mpp) REVERT: G 182 VAL cc_start: 0.6854 (p) cc_final: 0.6561 (m) REVERT: G 205 ARG cc_start: 0.5369 (tpp-160) cc_final: 0.4109 (ptm160) REVERT: G 439 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7992 (tm-30) REVERT: G 482 THR cc_start: 0.7525 (p) cc_final: 0.7156 (p) REVERT: q 39 HIS cc_start: 0.8109 (t-170) cc_final: 0.7668 (t-170) REVERT: q 133 MET cc_start: 0.8997 (mtp) cc_final: 0.8655 (mtm) REVERT: q 161 LYS cc_start: 0.9328 (mttt) cc_final: 0.9025 (mttm) REVERT: q 179 SER cc_start: 0.7347 (p) cc_final: 0.6955 (t) REVERT: q 273 MET cc_start: -0.2987 (tpt) cc_final: -0.3236 (tpt) REVERT: q 432 SER cc_start: 0.8845 (m) cc_final: 0.8512 (p) REVERT: q 474 VAL cc_start: 0.8895 (t) cc_final: 0.8679 (t) REVERT: q 479 TYR cc_start: 0.8335 (m-10) cc_final: 0.7918 (m-10) REVERT: q 511 ASP cc_start: 0.8160 (t0) cc_final: 0.7419 (t0) REVERT: Q 55 ILE cc_start: 0.8812 (mt) cc_final: 0.8584 (mt) REVERT: Q 83 LYS cc_start: 0.7083 (mtmt) cc_final: 0.6238 (tptt) REVERT: Q 92 GLN cc_start: 0.8201 (mm-40) cc_final: 0.6971 (mm-40) REVERT: Q 106 LEU cc_start: 0.9418 (mm) cc_final: 0.9135 (mm) REVERT: Q 120 MET cc_start: 0.6678 (mtt) cc_final: 0.6394 (mtm) REVERT: Q 431 ILE cc_start: 0.8831 (mm) cc_final: 0.8398 (mm) REVERT: Q 530 VAL cc_start: 0.9471 (t) cc_final: 0.9197 (p) REVERT: Q 533 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7021 (tm-30) REVERT: z 126 ARG cc_start: 0.7158 (ttp80) cc_final: 0.6574 (tpm170) REVERT: z 137 LYS cc_start: 0.7188 (pttt) cc_final: 0.6929 (pttt) REVERT: z 151 LEU cc_start: 0.7993 (mt) cc_final: 0.7760 (mt) REVERT: z 197 MET cc_start: 0.6364 (tpp) cc_final: 0.6087 (mmm) REVERT: z 224 MET cc_start: 0.2480 (mmp) cc_final: -0.1016 (mtm) REVERT: z 380 ILE cc_start: 0.7374 (mt) cc_final: 0.7000 (mt) REVERT: z 430 ASN cc_start: 0.2406 (OUTLIER) cc_final: 0.2205 (t0) REVERT: Z 43 LEU cc_start: 0.7728 (tp) cc_final: 0.7245 (tt) REVERT: Z 193 MET cc_start: 0.7506 (ppp) cc_final: 0.6607 (tmm) REVERT: Z 287 MET cc_start: 0.4382 (tpt) cc_final: 0.3766 (tpt) REVERT: h 38 GLU cc_start: 0.8060 (tp30) cc_final: 0.7250 (tm-30) REVERT: h 163 ARG cc_start: 0.5592 (mmp80) cc_final: 0.4144 (tpp80) REVERT: h 268 GLN cc_start: 0.4232 (mm110) cc_final: 0.3375 (pm20) REVERT: h 355 MET cc_start: 0.4207 (ppp) cc_final: 0.3520 (tpp) REVERT: h 418 MET cc_start: 0.7823 (mmm) cc_final: 0.7620 (mmm) REVERT: h 447 GLU cc_start: 0.7773 (mp0) cc_final: 0.7012 (mp0) REVERT: h 451 ARG cc_start: 0.8740 (ttm110) cc_final: 0.8503 (ttm110) REVERT: h 456 ASN cc_start: 0.8079 (m-40) cc_final: 0.7855 (m-40) REVERT: h 463 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7168 (tp30) REVERT: h 521 ASP cc_start: 0.8625 (m-30) cc_final: 0.8397 (m-30) REVERT: H 90 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6789 (tp40) REVERT: H 126 MET cc_start: 0.7446 (mtm) cc_final: 0.7162 (mtm) REVERT: H 166 MET cc_start: 0.4935 (mmt) cc_final: 0.4550 (mmt) REVERT: H 249 GLU cc_start: 0.0355 (pm20) cc_final: -0.1632 (tp30) REVERT: H 398 MET cc_start: 0.6809 (mtp) cc_final: 0.6220 (mtp) REVERT: H 447 GLU cc_start: 0.8032 (mp0) cc_final: 0.7600 (mp0) REVERT: H 467 LYS cc_start: 0.8152 (ttpt) cc_final: 0.7717 (ttpt) REVERT: H 490 ASP cc_start: 0.7035 (t0) cc_final: 0.6263 (p0) REVERT: H 504 ILE cc_start: 0.8767 (mt) cc_final: 0.8507 (mt) REVERT: H 515 ASN cc_start: 0.8506 (m-40) cc_final: 0.7079 (m-40) outliers start: 7 outliers final: 1 residues processed: 1522 average time/residue: 0.5494 time to fit residues: 1423.4331 Evaluate side-chains 1148 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1145 time to evaluate : 5.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 714 optimal weight: 0.0970 chunk 543 optimal weight: 0.9980 chunk 375 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 345 optimal weight: 2.9990 chunk 485 optimal weight: 5.9990 chunk 725 optimal weight: 5.9990 chunk 768 optimal weight: 0.0020 chunk 379 optimal weight: 9.9990 chunk 687 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 141 ASN a 514 HIS A 29 ASN A 77 HIS ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS d 395 HIS d 499 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 72 HIS g 123 GLN g 166 HIS ** g 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 GLN q 39 HIS ** q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 446 GLN ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 GLN Q 258 ASN ** z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 200 GLN ** Z 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 29 ASN h 305 GLN ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 61671 Z= 0.142 Angle : 0.518 10.786 83183 Z= 0.264 Chirality : 0.042 0.208 10018 Planarity : 0.003 0.044 10682 Dihedral : 3.668 24.819 8441 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.64 % Favored : 97.28 % Rotamer: Outliers : 0.04 % Allowed : 1.90 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.09), residues: 7946 helix: 0.30 (0.08), residues: 3710 sheet: -0.27 (0.20), residues: 617 loop : -0.79 (0.09), residues: 3619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP g 167 HIS 0.010 0.001 HIS e 197 PHE 0.033 0.001 PHE h 307 TYR 0.034 0.001 TYR h 226 ARG 0.007 0.000 ARG D 520 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1453 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1450 time to evaluate : 5.342 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 96 ASP cc_start: 0.6454 (m-30) cc_final: 0.6144 (m-30) REVERT: a 125 ILE cc_start: 0.9665 (mm) cc_final: 0.9298 (tp) REVERT: a 316 MET cc_start: 0.2019 (mtp) cc_final: 0.1447 (tpt) REVERT: a 471 SER cc_start: 0.9465 (m) cc_final: 0.8998 (t) REVERT: a 545 ILE cc_start: 0.8160 (mt) cc_final: 0.7914 (mp) REVERT: A 27 ASN cc_start: 0.7606 (m-40) cc_final: 0.7392 (m-40) REVERT: A 73 LEU cc_start: 0.6329 (tp) cc_final: 0.5666 (tt) REVERT: A 88 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7141 (mm110) REVERT: A 107 GLU cc_start: 0.8485 (tp30) cc_final: 0.8166 (tp30) REVERT: A 179 MET cc_start: 0.6201 (mmm) cc_final: 0.5940 (mmp) REVERT: A 233 MET cc_start: 0.4254 (tpp) cc_final: 0.3599 (tpp) REVERT: A 532 LEU cc_start: 0.9072 (mp) cc_final: 0.8414 (tt) REVERT: b 31 ASP cc_start: 0.7531 (m-30) cc_final: 0.7084 (m-30) REVERT: b 36 THR cc_start: 0.8905 (p) cc_final: 0.8459 (t) REVERT: b 78 VAL cc_start: 0.7131 (t) cc_final: 0.5561 (p) REVERT: b 98 LEU cc_start: 0.8758 (tp) cc_final: 0.8365 (tt) REVERT: b 347 MET cc_start: 0.5568 (mpp) cc_final: 0.5365 (mpp) REVERT: B 31 ASP cc_start: 0.7952 (p0) cc_final: 0.7719 (p0) REVERT: B 263 LYS cc_start: 0.7311 (mttt) cc_final: 0.6824 (tptp) REVERT: B 413 LYS cc_start: 0.8554 (pttt) cc_final: 0.7917 (mmtm) REVERT: B 451 ASP cc_start: 0.7306 (t0) cc_final: 0.6902 (t0) REVERT: d 20 VAL cc_start: 0.8623 (t) cc_final: 0.8329 (t) REVERT: d 30 SER cc_start: 0.8910 (m) cc_final: 0.8388 (t) REVERT: d 47 MET cc_start: 0.6826 (tmm) cc_final: 0.6384 (tmm) REVERT: d 77 MET cc_start: 0.8138 (mtp) cc_final: 0.7872 (mtp) REVERT: d 118 THR cc_start: 0.8572 (m) cc_final: 0.8294 (m) REVERT: d 138 MET cc_start: 0.5738 (mmt) cc_final: 0.5334 (mmt) REVERT: d 436 GLN cc_start: 0.8720 (pp30) cc_final: 0.8240 (pp30) REVERT: d 502 LEU cc_start: 0.8869 (tp) cc_final: 0.8580 (tp) REVERT: d 513 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7675 (tt0) REVERT: D 25 ILE cc_start: 0.9330 (mt) cc_final: 0.9006 (tt) REVERT: D 155 SER cc_start: 0.7614 (t) cc_final: 0.6981 (p) REVERT: D 385 MET cc_start: 0.3137 (ppp) cc_final: 0.2648 (pmm) REVERT: D 441 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8150 (mm-40) REVERT: D 469 LEU cc_start: 0.8344 (mt) cc_final: 0.8109 (mt) REVERT: e 146 ILE cc_start: 0.9289 (mt) cc_final: 0.9041 (mt) REVERT: e 238 LYS cc_start: 0.2385 (pptt) cc_final: 0.1933 (tttm) REVERT: e 450 MET cc_start: 0.8522 (mmm) cc_final: 0.8291 (mmt) REVERT: e 452 LEU cc_start: 0.9115 (pp) cc_final: 0.8901 (tt) REVERT: e 474 GLN cc_start: 0.8083 (tp40) cc_final: 0.7681 (tp40) REVERT: e 481 MET cc_start: 0.9133 (mmm) cc_final: 0.8770 (tpp) REVERT: E 112 ASP cc_start: 0.7042 (p0) cc_final: 0.6805 (p0) REVERT: E 212 MET cc_start: 0.6472 (ttp) cc_final: 0.6035 (ttp) REVERT: E 450 MET cc_start: 0.8474 (tpp) cc_final: 0.8084 (mmt) REVERT: E 495 LEU cc_start: 0.9365 (tp) cc_final: 0.9114 (tp) REVERT: E 552 ASP cc_start: 0.8216 (p0) cc_final: 0.7871 (p0) REVERT: g 102 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8580 (mm-30) REVERT: g 106 GLN cc_start: 0.6999 (tp-100) cc_final: 0.6679 (tp40) REVERT: g 116 ILE cc_start: 0.9087 (mt) cc_final: 0.8865 (tt) REVERT: g 126 LYS cc_start: 0.8281 (mmtt) cc_final: 0.8036 (mmtt) REVERT: g 234 MET cc_start: 0.1315 (mmm) cc_final: 0.0794 (mmm) REVERT: g 453 PRO cc_start: 0.9504 (Cg_exo) cc_final: 0.9287 (Cg_endo) REVERT: G 151 MET cc_start: 0.7462 (mpp) cc_final: 0.7108 (mpp) REVERT: G 182 VAL cc_start: 0.6780 (p) cc_final: 0.6458 (m) REVERT: G 205 ARG cc_start: 0.5118 (tpp-160) cc_final: 0.4140 (ptm160) REVERT: G 412 LEU cc_start: 0.6200 (tp) cc_final: 0.5353 (tp) REVERT: G 421 MET cc_start: 0.7213 (ttt) cc_final: 0.6377 (ttt) REVERT: G 449 MET cc_start: 0.8969 (tpp) cc_final: 0.8599 (tpp) REVERT: G 482 THR cc_start: 0.7637 (p) cc_final: 0.7312 (p) REVERT: q 104 MET cc_start: 0.8444 (mmm) cc_final: 0.8231 (tpp) REVERT: q 154 ASN cc_start: 0.6427 (m-40) cc_final: 0.5384 (t0) REVERT: q 161 LYS cc_start: 0.9249 (mttt) cc_final: 0.8923 (mttm) REVERT: q 179 SER cc_start: 0.7532 (p) cc_final: 0.7232 (t) REVERT: q 395 ASP cc_start: 0.7634 (p0) cc_final: 0.7055 (p0) REVERT: q 445 LEU cc_start: 0.8459 (mm) cc_final: 0.7732 (mm) REVERT: q 505 SER cc_start: 0.6904 (t) cc_final: 0.6471 (p) REVERT: q 511 ASP cc_start: 0.7971 (t0) cc_final: 0.7205 (t0) REVERT: Q 55 ILE cc_start: 0.8706 (mt) cc_final: 0.8501 (mt) REVERT: Q 83 LYS cc_start: 0.6955 (mtmt) cc_final: 0.6212 (tptt) REVERT: Q 92 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7755 (mm-40) REVERT: Q 98 ASP cc_start: 0.6248 (t0) cc_final: 0.5924 (t0) REVERT: Q 120 MET cc_start: 0.6654 (mtt) cc_final: 0.6445 (mtm) REVERT: Q 431 ILE cc_start: 0.8748 (mm) cc_final: 0.8277 (mm) REVERT: Q 519 ASP cc_start: 0.8392 (m-30) cc_final: 0.7985 (m-30) REVERT: Q 528 ILE cc_start: 0.9170 (mm) cc_final: 0.8916 (mm) REVERT: Q 530 VAL cc_start: 0.9488 (t) cc_final: 0.9214 (p) REVERT: z 126 ARG cc_start: 0.7067 (ttp80) cc_final: 0.6674 (tpm170) REVERT: z 224 MET cc_start: 0.2466 (mmp) cc_final: -0.1021 (mtm) REVERT: z 380 ILE cc_start: 0.7280 (mt) cc_final: 0.6995 (mt) REVERT: Z 43 LEU cc_start: 0.7653 (tp) cc_final: 0.7188 (tt) REVERT: Z 46 LEU cc_start: 0.8683 (mt) cc_final: 0.8444 (mt) REVERT: Z 193 MET cc_start: 0.7483 (ppp) cc_final: 0.6627 (tmm) REVERT: Z 229 LYS cc_start: 0.7356 (tppt) cc_final: 0.6856 (tptt) REVERT: Z 287 MET cc_start: 0.4226 (tpt) cc_final: 0.3860 (tpt) REVERT: Z 422 LEU cc_start: 0.9226 (tp) cc_final: 0.8983 (tt) REVERT: Z 504 GLU cc_start: 0.8275 (tp30) cc_final: 0.7981 (tp30) REVERT: h 38 GLU cc_start: 0.7944 (tp30) cc_final: 0.7404 (tm-30) REVERT: h 216 ASN cc_start: 0.7573 (p0) cc_final: 0.6460 (t0) REVERT: h 268 GLN cc_start: 0.4252 (mm110) cc_final: 0.3372 (pm20) REVERT: h 307 PHE cc_start: 0.4978 (m-80) cc_final: 0.4618 (m-80) REVERT: h 355 MET cc_start: 0.4088 (ppp) cc_final: 0.3838 (tpp) REVERT: h 447 GLU cc_start: 0.8076 (mp0) cc_final: 0.7123 (mp0) REVERT: h 463 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6984 (tp30) REVERT: h 515 ASN cc_start: 0.8032 (m-40) cc_final: 0.7823 (m-40) REVERT: H 108 LEU cc_start: 0.7794 (mt) cc_final: 0.7511 (mt) REVERT: H 166 MET cc_start: 0.5081 (mmt) cc_final: 0.4694 (mmt) REVERT: H 490 ASP cc_start: 0.6799 (t0) cc_final: 0.6119 (p0) REVERT: H 504 ILE cc_start: 0.8849 (mt) cc_final: 0.8615 (mt) REVERT: H 515 ASN cc_start: 0.8502 (m-40) cc_final: 0.7229 (m-40) outliers start: 3 outliers final: 0 residues processed: 1451 average time/residue: 0.5394 time to fit residues: 1341.4862 Evaluate side-chains 1116 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1116 time to evaluate : 5.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 639 optimal weight: 6.9990 chunk 436 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 572 optimal weight: 20.0000 chunk 317 optimal weight: 5.9990 chunk 655 optimal weight: 2.9990 chunk 531 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 392 optimal weight: 6.9990 chunk 689 optimal weight: 0.3980 chunk 193 optimal weight: 1.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 209 HIS ** a 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 514 HIS A 90 GLN b 393 GLN ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 395 HIS ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 466 GLN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 HIS ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 GLN ** G 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 39 HIS ** q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 92 GLN ** q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 477 ASN ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 HIS ** z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 29 ASN h 472 HIS ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN H 232 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.6606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 61671 Z= 0.201 Angle : 0.577 12.149 83183 Z= 0.297 Chirality : 0.043 0.206 10018 Planarity : 0.004 0.069 10682 Dihedral : 3.987 28.236 8441 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.36 % Favored : 96.56 % Rotamer: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.09), residues: 7946 helix: 0.46 (0.08), residues: 3719 sheet: -0.42 (0.20), residues: 632 loop : -0.80 (0.10), residues: 3595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP g 167 HIS 0.011 0.001 HIS E 50 PHE 0.027 0.002 PHE h 307 TYR 0.023 0.002 TYR h 226 ARG 0.013 0.001 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1432 time to evaluate : 6.826 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 125 ILE cc_start: 0.9702 (mm) cc_final: 0.9298 (tp) REVERT: a 197 LYS cc_start: 0.4104 (mtpt) cc_final: 0.3813 (mmtp) REVERT: a 198 TYR cc_start: 0.4202 (m-80) cc_final: 0.3753 (m-80) REVERT: a 233 MET cc_start: 0.0275 (mtp) cc_final: 0.0009 (mtp) REVERT: a 244 ILE cc_start: 0.7904 (mp) cc_final: 0.7591 (mp) REVERT: a 316 MET cc_start: 0.2087 (mtp) cc_final: 0.1759 (tpt) REVERT: a 398 MET cc_start: 0.1614 (mmp) cc_final: 0.1225 (mmm) REVERT: a 455 LEU cc_start: 0.9628 (mm) cc_final: 0.9402 (mm) REVERT: a 460 LYS cc_start: 0.9369 (tttp) cc_final: 0.9043 (ttmm) REVERT: a 471 SER cc_start: 0.9466 (m) cc_final: 0.9080 (t) REVERT: a 545 ILE cc_start: 0.8608 (mt) cc_final: 0.8298 (mp) REVERT: A 19 LYS cc_start: 0.8135 (pptt) cc_final: 0.7877 (pttt) REVERT: A 27 ASN cc_start: 0.8018 (m-40) cc_final: 0.7518 (m-40) REVERT: A 44 LEU cc_start: 0.9149 (tt) cc_final: 0.8938 (tt) REVERT: A 107 GLU cc_start: 0.8503 (tp30) cc_final: 0.8249 (tp30) REVERT: A 233 MET cc_start: 0.4739 (tpp) cc_final: 0.4090 (tpp) REVERT: A 532 LEU cc_start: 0.9230 (mp) cc_final: 0.8189 (tt) REVERT: b 31 ASP cc_start: 0.7607 (m-30) cc_final: 0.7214 (m-30) REVERT: b 36 THR cc_start: 0.9037 (p) cc_final: 0.8653 (t) REVERT: b 47 GLN cc_start: 0.7288 (pp30) cc_final: 0.6894 (pp30) REVERT: b 101 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7881 (mm-30) REVERT: b 111 ASP cc_start: 0.6680 (p0) cc_final: 0.6454 (p0) REVERT: b 120 ILE cc_start: 0.8305 (mt) cc_final: 0.7958 (mm) REVERT: b 454 GLU cc_start: 0.5719 (tm-30) cc_final: 0.4752 (tm-30) REVERT: B 31 ASP cc_start: 0.7958 (p0) cc_final: 0.7696 (p0) REVERT: B 105 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6590 (mm-30) REVERT: B 137 LYS cc_start: 0.6889 (pttp) cc_final: 0.6055 (tmtt) REVERT: B 263 LYS cc_start: 0.7246 (mttt) cc_final: 0.6799 (tptp) REVERT: B 413 LYS cc_start: 0.8852 (pttt) cc_final: 0.8007 (mmtt) REVERT: B 425 LYS cc_start: 0.7466 (mmpt) cc_final: 0.6632 (mmtt) REVERT: B 451 ASP cc_start: 0.7386 (t0) cc_final: 0.7153 (t0) REVERT: B 458 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7786 (mmmt) REVERT: d 30 SER cc_start: 0.8986 (m) cc_final: 0.8556 (t) REVERT: d 47 MET cc_start: 0.7583 (tmm) cc_final: 0.6993 (tmm) REVERT: d 108 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6966 (mt-10) REVERT: d 118 THR cc_start: 0.8883 (m) cc_final: 0.8677 (m) REVERT: d 133 ASP cc_start: 0.7442 (m-30) cc_final: 0.7087 (m-30) REVERT: d 190 ASP cc_start: 0.5898 (t70) cc_final: 0.5588 (t70) REVERT: d 436 GLN cc_start: 0.8825 (pp30) cc_final: 0.8534 (pp30) REVERT: d 502 LEU cc_start: 0.8753 (tp) cc_final: 0.8537 (tp) REVERT: D 25 ILE cc_start: 0.9402 (mt) cc_final: 0.9075 (tt) REVERT: D 118 THR cc_start: 0.9200 (m) cc_final: 0.8994 (t) REVERT: D 132 VAL cc_start: 0.9048 (t) cc_final: 0.8750 (t) REVERT: e 135 GLU cc_start: 0.8201 (mp0) cc_final: 0.7933 (mp0) REVERT: e 146 ILE cc_start: 0.9497 (mt) cc_final: 0.9284 (mt) REVERT: e 428 CYS cc_start: 0.7377 (m) cc_final: 0.6999 (m) REVERT: e 429 VAL cc_start: 0.8055 (t) cc_final: 0.7850 (t) REVERT: e 450 MET cc_start: 0.8546 (mmm) cc_final: 0.8304 (mmt) REVERT: e 452 LEU cc_start: 0.9246 (pp) cc_final: 0.8961 (tt) REVERT: e 474 GLN cc_start: 0.8143 (tp40) cc_final: 0.7678 (tp40) REVERT: e 481 MET cc_start: 0.9252 (mmm) cc_final: 0.8805 (tpp) REVERT: e 522 MET cc_start: 0.7039 (ppp) cc_final: 0.6809 (ppp) REVERT: E 68 ARG cc_start: 0.6908 (ttt-90) cc_final: 0.5696 (ttt-90) REVERT: E 112 ASP cc_start: 0.7183 (p0) cc_final: 0.6968 (p0) REVERT: E 212 MET cc_start: 0.6400 (ttp) cc_final: 0.5884 (ttp) REVERT: E 391 ARG cc_start: 0.5819 (mmp80) cc_final: 0.4232 (mtm180) REVERT: E 531 PHE cc_start: 0.7704 (t80) cc_final: 0.7471 (t80) REVERT: E 552 ASP cc_start: 0.8346 (p0) cc_final: 0.8106 (p0) REVERT: E 553 ASN cc_start: 0.8302 (m110) cc_final: 0.8022 (m110) REVERT: g 102 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8659 (mm-30) REVERT: g 106 GLN cc_start: 0.7221 (tp-100) cc_final: 0.7010 (tp40) REVERT: g 126 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7967 (mmtt) REVERT: g 249 PRO cc_start: 0.3195 (Cg_endo) cc_final: 0.2891 (Cg_exo) REVERT: g 277 GLU cc_start: 0.5426 (mt-10) cc_final: 0.5121 (tp30) REVERT: g 524 ASP cc_start: 0.7186 (p0) cc_final: 0.6778 (p0) REVERT: g 525 ASP cc_start: 0.7863 (p0) cc_final: 0.7654 (p0) REVERT: G 39 LEU cc_start: 0.7791 (tp) cc_final: 0.7421 (tp) REVERT: G 151 MET cc_start: 0.7497 (mpp) cc_final: 0.6725 (mpp) REVERT: G 404 ARG cc_start: 0.6444 (ptm160) cc_final: 0.6219 (tmt-80) REVERT: G 406 VAL cc_start: 0.7982 (t) cc_final: 0.7735 (t) REVERT: G 412 LEU cc_start: 0.5999 (tp) cc_final: 0.5309 (tp) REVERT: G 421 MET cc_start: 0.7601 (ttt) cc_final: 0.6768 (ttt) REVERT: G 449 MET cc_start: 0.9087 (tpp) cc_final: 0.8757 (tpp) REVERT: G 466 ARG cc_start: 0.8600 (mtp180) cc_final: 0.8316 (tpp-160) REVERT: G 482 THR cc_start: 0.7688 (p) cc_final: 0.7423 (p) REVERT: q 46 MET cc_start: 0.3627 (tpt) cc_final: 0.2939 (tpt) REVERT: q 133 MET cc_start: 0.8973 (mtp) cc_final: 0.8530 (mtm) REVERT: q 161 LYS cc_start: 0.9290 (mttt) cc_final: 0.8964 (mtpt) REVERT: q 179 SER cc_start: 0.7689 (p) cc_final: 0.7437 (t) REVERT: q 395 ASP cc_start: 0.7885 (p0) cc_final: 0.7106 (p0) REVERT: q 432 SER cc_start: 0.8841 (m) cc_final: 0.8337 (p) REVERT: q 444 LEU cc_start: 0.8899 (mt) cc_final: 0.8698 (mp) REVERT: q 445 LEU cc_start: 0.8764 (mm) cc_final: 0.8265 (mm) REVERT: q 450 LYS cc_start: 0.8915 (mttt) cc_final: 0.8617 (mttt) REVERT: q 511 ASP cc_start: 0.7929 (t0) cc_final: 0.6863 (t0) REVERT: q 546 MET cc_start: 0.4526 (mmm) cc_final: 0.3899 (mmm) REVERT: Q 46 MET cc_start: 0.6920 (ttp) cc_final: 0.6669 (ttp) REVERT: Q 55 ILE cc_start: 0.8991 (mt) cc_final: 0.8752 (mt) REVERT: Q 92 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8042 (mm-40) REVERT: Q 98 ASP cc_start: 0.5975 (t0) cc_final: 0.5625 (t0) REVERT: Q 431 ILE cc_start: 0.8954 (mm) cc_final: 0.8302 (mm) REVERT: Q 530 VAL cc_start: 0.9532 (t) cc_final: 0.9248 (p) REVERT: z 61 VAL cc_start: 0.8331 (p) cc_final: 0.7758 (p) REVERT: z 134 ASP cc_start: 0.7733 (t0) cc_final: 0.7419 (t0) REVERT: z 137 LYS cc_start: 0.7309 (pttt) cc_final: 0.6681 (pttt) REVERT: z 224 MET cc_start: 0.2765 (mmp) cc_final: -0.0734 (mtm) REVERT: Z 43 LEU cc_start: 0.7718 (tp) cc_final: 0.6916 (tt) REVERT: Z 46 LEU cc_start: 0.8827 (mt) cc_final: 0.8578 (mt) REVERT: Z 113 VAL cc_start: 0.8657 (t) cc_final: 0.7550 (p) REVERT: Z 130 MET cc_start: 0.7732 (mmp) cc_final: 0.7242 (tpp) REVERT: Z 193 MET cc_start: 0.7473 (ppp) cc_final: 0.6664 (tmm) REVERT: Z 229 LYS cc_start: 0.7472 (tppt) cc_final: 0.7046 (tptt) REVERT: Z 279 ASP cc_start: 0.7099 (m-30) cc_final: 0.6871 (m-30) REVERT: Z 287 MET cc_start: 0.4449 (tpt) cc_final: 0.3930 (tpt) REVERT: Z 439 LYS cc_start: 0.7711 (tptt) cc_final: 0.7463 (tptm) REVERT: Z 504 GLU cc_start: 0.8367 (tp30) cc_final: 0.8030 (tp30) REVERT: h 38 GLU cc_start: 0.8025 (tp30) cc_final: 0.6946 (tm-30) REVERT: h 59 LYS cc_start: 0.7439 (tppt) cc_final: 0.7205 (tppt) REVERT: h 216 ASN cc_start: 0.7661 (p0) cc_final: 0.6436 (t0) REVERT: h 268 GLN cc_start: 0.4539 (mm110) cc_final: 0.3536 (pm20) REVERT: h 418 MET cc_start: 0.8443 (mmm) cc_final: 0.8135 (mmm) REVERT: h 447 GLU cc_start: 0.8321 (mp0) cc_final: 0.7643 (mp0) REVERT: h 455 GLU cc_start: 0.7850 (pp20) cc_final: 0.7485 (pp20) REVERT: h 463 GLU cc_start: 0.7615 (mm-30) cc_final: 0.6985 (tp30) REVERT: h 483 PHE cc_start: 0.4890 (m-10) cc_final: 0.4313 (m-80) REVERT: H 121 SER cc_start: 0.8466 (t) cc_final: 0.8196 (p) REVERT: H 126 MET cc_start: 0.7917 (mtp) cc_final: 0.7675 (mtp) REVERT: H 166 MET cc_start: 0.5120 (mmt) cc_final: 0.4692 (mmt) REVERT: H 417 GLU cc_start: 0.8782 (pm20) cc_final: 0.8405 (pm20) REVERT: H 490 ASP cc_start: 0.7261 (t0) cc_final: 0.6537 (p0) REVERT: H 504 ILE cc_start: 0.8895 (mt) cc_final: 0.8680 (mt) outliers start: 2 outliers final: 0 residues processed: 1433 average time/residue: 0.5407 time to fit residues: 1331.2368 Evaluate side-chains 1134 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1134 time to evaluate : 5.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 258 optimal weight: 4.9990 chunk 692 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 451 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 chunk 769 optimal weight: 0.0980 chunk 638 optimal weight: 0.7980 chunk 356 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 254 optimal weight: 3.9990 chunk 403 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 514 HIS ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS A 90 GLN b 447 ASN ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 395 HIS ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 466 GLN e 536 GLN E 210 ASN E 553 ASN g 123 GLN ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 HIS ** q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 92 GLN ** q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 152 GLN ** z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 356 GLN z 404 ASN ** Z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 201 HIS Z 356 GLN ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 29 ASN ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 291 ASN h 305 GLN ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.6815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 61671 Z= 0.146 Angle : 0.535 11.315 83183 Z= 0.271 Chirality : 0.042 0.236 10018 Planarity : 0.003 0.050 10682 Dihedral : 3.801 28.506 8441 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 0.01 % Allowed : 1.32 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.09), residues: 7946 helix: 0.65 (0.08), residues: 3737 sheet: -0.32 (0.20), residues: 655 loop : -0.75 (0.10), residues: 3554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP g 167 HIS 0.008 0.001 HIS G 72 PHE 0.025 0.001 PHE h 307 TYR 0.027 0.001 TYR Z 355 ARG 0.015 0.000 ARG g 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1433 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1432 time to evaluate : 6.702 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: a 53 LEU cc_start: 0.7930 (mp) cc_final: 0.7607 (mp) REVERT: a 96 ASP cc_start: 0.6119 (m-30) cc_final: 0.5831 (m-30) REVERT: a 108 LEU cc_start: 0.8819 (mm) cc_final: 0.8458 (mm) REVERT: a 114 GLU cc_start: 0.7649 (pp20) cc_final: 0.7147 (pp20) REVERT: a 125 ILE cc_start: 0.9621 (mm) cc_final: 0.9182 (tp) REVERT: a 130 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7979 (mmm-85) REVERT: a 197 LYS cc_start: 0.4075 (mtpt) cc_final: 0.3784 (mmtp) REVERT: a 233 MET cc_start: 0.0628 (mtp) cc_final: 0.0287 (mtp) REVERT: a 316 MET cc_start: 0.1816 (mtp) cc_final: 0.1591 (tpt) REVERT: a 443 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7514 (mtp85) REVERT: a 460 LYS cc_start: 0.9341 (tttp) cc_final: 0.8998 (ttmm) REVERT: a 471 SER cc_start: 0.9452 (m) cc_final: 0.9017 (t) REVERT: a 545 ILE cc_start: 0.8608 (mt) cc_final: 0.8390 (mp) REVERT: A 19 LYS cc_start: 0.8399 (pptt) cc_final: 0.8106 (pttt) REVERT: A 44 LEU cc_start: 0.9108 (tt) cc_final: 0.8854 (tt) REVERT: A 73 LEU cc_start: 0.6717 (tp) cc_final: 0.6083 (tt) REVERT: A 88 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7078 (mm110) REVERT: A 107 GLU cc_start: 0.8502 (tp30) cc_final: 0.8133 (tp30) REVERT: A 118 ASN cc_start: 0.8453 (m110) cc_final: 0.8167 (m110) REVERT: A 233 MET cc_start: 0.4541 (tpp) cc_final: 0.3892 (tpp) REVERT: A 478 ARG cc_start: 0.7752 (mtp-110) cc_final: 0.7390 (mtp-110) REVERT: A 532 LEU cc_start: 0.9093 (mp) cc_final: 0.8290 (tt) REVERT: b 31 ASP cc_start: 0.7708 (m-30) cc_final: 0.7275 (m-30) REVERT: b 36 THR cc_start: 0.9049 (p) cc_final: 0.8713 (t) REVERT: b 47 GLN cc_start: 0.7299 (pp30) cc_final: 0.6810 (pp30) REVERT: b 78 VAL cc_start: 0.6863 (t) cc_final: 0.5578 (t) REVERT: b 101 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7865 (mm-30) REVERT: b 120 ILE cc_start: 0.8288 (mt) cc_final: 0.7912 (mm) REVERT: B 31 ASP cc_start: 0.7913 (p0) cc_final: 0.7604 (p0) REVERT: B 42 MET cc_start: 0.7430 (tpt) cc_final: 0.7141 (tpt) REVERT: B 105 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6807 (mm-30) REVERT: B 121 ILE cc_start: 0.8260 (mm) cc_final: 0.7884 (mm) REVERT: B 137 LYS cc_start: 0.6883 (pttp) cc_final: 0.5934 (tmtt) REVERT: B 263 LYS cc_start: 0.7413 (mttt) cc_final: 0.6923 (tptp) REVERT: B 413 LYS cc_start: 0.8772 (pttt) cc_final: 0.7972 (mmtm) REVERT: B 451 ASP cc_start: 0.7191 (t0) cc_final: 0.6934 (t0) REVERT: d 30 SER cc_start: 0.8959 (m) cc_final: 0.8480 (t) REVERT: d 47 MET cc_start: 0.7595 (tmm) cc_final: 0.7011 (tmm) REVERT: d 118 THR cc_start: 0.8526 (m) cc_final: 0.8292 (m) REVERT: d 138 MET cc_start: 0.6447 (mmm) cc_final: 0.5758 (mpp) REVERT: d 190 ASP cc_start: 0.5887 (t70) cc_final: 0.5649 (t70) REVERT: d 284 ASN cc_start: 0.5559 (t0) cc_final: 0.4494 (m-40) REVERT: d 502 LEU cc_start: 0.8793 (tp) cc_final: 0.8589 (tp) REVERT: d 520 ARG cc_start: 0.8461 (mtp85) cc_final: 0.8197 (mtt-85) REVERT: D 25 ILE cc_start: 0.9445 (mt) cc_final: 0.9106 (tt) REVERT: D 118 THR cc_start: 0.9113 (m) cc_final: 0.8847 (t) REVERT: D 155 SER cc_start: 0.7629 (t) cc_final: 0.6975 (p) REVERT: D 385 MET cc_start: 0.3609 (ppp) cc_final: 0.3016 (pmm) REVERT: D 520 ARG cc_start: 0.8307 (mmm-85) cc_final: 0.8101 (mmm-85) REVERT: e 146 ILE cc_start: 0.9496 (mt) cc_final: 0.9296 (mt) REVERT: e 203 MET cc_start: 0.6404 (tmm) cc_final: 0.5995 (tmm) REVERT: e 238 LYS cc_start: 0.2842 (pptt) cc_final: 0.2424 (tttm) REVERT: e 428 CYS cc_start: 0.7321 (m) cc_final: 0.7039 (m) REVERT: e 474 GLN cc_start: 0.8017 (tp40) cc_final: 0.7745 (tp40) REVERT: e 481 MET cc_start: 0.9239 (mmm) cc_final: 0.8857 (tpt) REVERT: E 68 ARG cc_start: 0.6768 (ttt-90) cc_final: 0.5734 (ttt-90) REVERT: E 112 ASP cc_start: 0.7106 (p0) cc_final: 0.6864 (p0) REVERT: E 212 MET cc_start: 0.6255 (ttp) cc_final: 0.5822 (ttp) REVERT: E 552 ASP cc_start: 0.8379 (p0) cc_final: 0.7948 (p0) REVERT: E 553 ASN cc_start: 0.8435 (m-40) cc_final: 0.8011 (m-40) REVERT: g 106 GLN cc_start: 0.7171 (tp-100) cc_final: 0.6964 (tp40) REVERT: g 234 MET cc_start: 0.1465 (mmm) cc_final: 0.0895 (mmm) REVERT: g 277 GLU cc_start: 0.5430 (mt-10) cc_final: 0.5083 (tp30) REVERT: g 359 MET cc_start: 0.4429 (ppp) cc_final: 0.4094 (ppp) REVERT: g 453 PRO cc_start: 0.9575 (Cg_exo) cc_final: 0.9324 (Cg_endo) REVERT: g 494 MET cc_start: 0.5362 (tpp) cc_final: 0.5131 (tpp) REVERT: g 524 ASP cc_start: 0.7390 (p0) cc_final: 0.6971 (p0) REVERT: G 39 LEU cc_start: 0.7810 (tp) cc_final: 0.7481 (tp) REVERT: G 151 MET cc_start: 0.7414 (mpp) cc_final: 0.6564 (mpp) REVERT: G 153 LYS cc_start: 0.7348 (mmpt) cc_final: 0.6962 (mppt) REVERT: G 234 MET cc_start: 0.3311 (ptp) cc_final: 0.2741 (mpp) REVERT: G 380 MET cc_start: 0.0573 (mpp) cc_final: -0.0351 (ttp) REVERT: G 412 LEU cc_start: 0.6632 (tp) cc_final: 0.5928 (tp) REVERT: G 466 ARG cc_start: 0.8606 (mtp180) cc_final: 0.8235 (mtp85) REVERT: q 126 GLU cc_start: 0.7266 (tp30) cc_final: 0.6809 (tp30) REVERT: q 133 MET cc_start: 0.8912 (mtp) cc_final: 0.8616 (mtp) REVERT: q 161 LYS cc_start: 0.9231 (mttt) cc_final: 0.9025 (mttm) REVERT: q 179 SER cc_start: 0.7844 (p) cc_final: 0.7515 (t) REVERT: q 432 SER cc_start: 0.8681 (m) cc_final: 0.8226 (p) REVERT: q 445 LEU cc_start: 0.8650 (mm) cc_final: 0.8250 (mm) REVERT: q 450 LYS cc_start: 0.8992 (mttt) cc_final: 0.8525 (mttt) REVERT: q 546 MET cc_start: 0.4496 (mmm) cc_final: 0.3962 (mmm) REVERT: Q 46 MET cc_start: 0.6859 (ttp) cc_final: 0.6646 (ttp) REVERT: Q 86 VAL cc_start: 0.9070 (t) cc_final: 0.8816 (t) REVERT: Q 92 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7888 (mm-40) REVERT: Q 98 ASP cc_start: 0.5888 (t0) cc_final: 0.5640 (t0) REVERT: Q 122 LEU cc_start: 0.8340 (tp) cc_final: 0.8097 (tp) REVERT: Q 431 ILE cc_start: 0.8789 (mm) cc_final: 0.8174 (mm) REVERT: Q 458 VAL cc_start: 0.8902 (p) cc_final: 0.8515 (p) REVERT: Q 528 ILE cc_start: 0.9276 (mm) cc_final: 0.9072 (mm) REVERT: Q 530 VAL cc_start: 0.9449 (t) cc_final: 0.9117 (p) REVERT: z 65 GLU cc_start: 0.6405 (mp0) cc_final: 0.6171 (mp0) REVERT: z 118 ILE cc_start: 0.8946 (mm) cc_final: 0.8737 (mm) REVERT: z 224 MET cc_start: 0.2805 (mmp) cc_final: -0.0648 (mtm) REVERT: z 380 ILE cc_start: 0.7741 (mt) cc_final: 0.7423 (mt) REVERT: z 406 LEU cc_start: 0.8621 (mp) cc_final: 0.8406 (mm) REVERT: Z 113 VAL cc_start: 0.8720 (t) cc_final: 0.7557 (p) REVERT: Z 130 MET cc_start: 0.7526 (mmp) cc_final: 0.7191 (tpp) REVERT: Z 152 GLN cc_start: 0.8340 (mt0) cc_final: 0.7891 (tt0) REVERT: Z 193 MET cc_start: 0.6946 (ppp) cc_final: 0.6443 (tmm) REVERT: Z 275 LYS cc_start: 0.6465 (mtmt) cc_final: 0.6180 (mtpt) REVERT: Z 279 ASP cc_start: 0.7135 (m-30) cc_final: 0.6862 (m-30) REVERT: Z 287 MET cc_start: 0.4268 (tpt) cc_final: 0.3812 (tpt) REVERT: Z 422 LEU cc_start: 0.9537 (tp) cc_final: 0.9127 (tt) REVERT: Z 424 ARG cc_start: 0.8066 (mtp-110) cc_final: 0.7630 (mtm180) REVERT: Z 439 LYS cc_start: 0.7936 (tptt) cc_final: 0.7630 (tptm) REVERT: Z 504 GLU cc_start: 0.8351 (tp30) cc_final: 0.7654 (tp30) REVERT: Z 506 ILE cc_start: 0.7785 (mt) cc_final: 0.7482 (mt) REVERT: h 38 GLU cc_start: 0.7978 (tp30) cc_final: 0.7761 (tp30) REVERT: h 59 LYS cc_start: 0.7562 (tppt) cc_final: 0.7249 (tppt) REVERT: h 216 ASN cc_start: 0.7838 (p0) cc_final: 0.6695 (t0) REVERT: h 268 GLN cc_start: 0.4499 (mm110) cc_final: 0.3458 (pm20) REVERT: h 447 GLU cc_start: 0.8061 (mp0) cc_final: 0.7589 (mp0) REVERT: h 452 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8122 (mm-40) REVERT: h 455 GLU cc_start: 0.7383 (pp20) cc_final: 0.6998 (pp20) REVERT: h 463 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6929 (tp30) REVERT: H 108 LEU cc_start: 0.8372 (mt) cc_final: 0.8117 (mt) REVERT: H 121 SER cc_start: 0.8560 (t) cc_final: 0.8262 (p) REVERT: H 166 MET cc_start: 0.5060 (mmt) cc_final: 0.4632 (mmt) REVERT: H 398 MET cc_start: 0.6176 (mtt) cc_final: 0.5844 (mtp) REVERT: H 490 ASP cc_start: 0.7180 (t0) cc_final: 0.6549 (p0) REVERT: H 504 ILE cc_start: 0.8880 (mt) cc_final: 0.8645 (mt) outliers start: 1 outliers final: 0 residues processed: 1433 average time/residue: 0.5463 time to fit residues: 1348.0875 Evaluate side-chains 1150 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1150 time to evaluate : 5.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 741 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 438 optimal weight: 5.9990 chunk 561 optimal weight: 6.9990 chunk 435 optimal weight: 0.0670 chunk 647 optimal weight: 4.9990 chunk 429 optimal weight: 2.9990 chunk 766 optimal weight: 2.9990 chunk 479 optimal weight: 8.9990 chunk 467 optimal weight: 20.0000 chunk 353 optimal weight: 5.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 499 ASN a 514 HIS A 209 HIS b 288 GLN ** d 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 395 HIS ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 HIS ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 466 GLN e 553 ASN g 166 HIS g 279 GLN ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 430 ASN ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 268 GLN ** h 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 472 HIS ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN H 232 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.7795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 61671 Z= 0.245 Angle : 0.647 15.612 83183 Z= 0.331 Chirality : 0.045 0.220 10018 Planarity : 0.004 0.053 10682 Dihedral : 4.408 36.710 8441 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 0.01 % Allowed : 1.62 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.09), residues: 7946 helix: 0.45 (0.08), residues: 3718 sheet: -0.50 (0.20), residues: 653 loop : -0.89 (0.10), residues: 3575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP g 167 HIS 0.012 0.001 HIS E 50 PHE 0.030 0.002 PHE B 149 TYR 0.022 0.002 TYR a 432 ARG 0.010 0.001 ARG Z 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1455 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1454 time to evaluate : 5.287 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: a 96 ASP cc_start: 0.6460 (m-30) cc_final: 0.6259 (m-30) REVERT: a 108 LEU cc_start: 0.9020 (mm) cc_final: 0.8759 (mm) REVERT: a 114 GLU cc_start: 0.7803 (pp20) cc_final: 0.7559 (pp20) REVERT: a 233 MET cc_start: 0.0412 (mtp) cc_final: 0.0149 (mtp) REVERT: a 316 MET cc_start: 0.2348 (mtp) cc_final: 0.1962 (tpt) REVERT: a 455 LEU cc_start: 0.9655 (mm) cc_final: 0.9358 (mm) REVERT: a 460 LYS cc_start: 0.9514 (tttp) cc_final: 0.9038 (ttmm) REVERT: a 471 SER cc_start: 0.9536 (m) cc_final: 0.9068 (t) REVERT: a 542 ASP cc_start: 0.8797 (p0) cc_final: 0.8473 (p0) REVERT: A 107 GLU cc_start: 0.8583 (tp30) cc_final: 0.8205 (tp30) REVERT: A 219 VAL cc_start: 0.2899 (p) cc_final: 0.2641 (p) REVERT: A 233 MET cc_start: 0.4860 (tpp) cc_final: 0.3859 (tpp) REVERT: A 532 LEU cc_start: 0.9123 (mp) cc_final: 0.8142 (tt) REVERT: A 540 ARG cc_start: 0.8380 (mtp85) cc_final: 0.7750 (mtp85) REVERT: b 36 THR cc_start: 0.9268 (p) cc_final: 0.8905 (t) REVERT: b 45 LEU cc_start: 0.8722 (tp) cc_final: 0.8447 (tp) REVERT: b 47 GLN cc_start: 0.7615 (pp30) cc_final: 0.7089 (pp30) REVERT: b 101 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7753 (mm-30) REVERT: B 31 ASP cc_start: 0.8211 (p0) cc_final: 0.7939 (p0) REVERT: B 105 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7330 (mm-30) REVERT: B 107 GLU cc_start: 0.8102 (pm20) cc_final: 0.7522 (pm20) REVERT: B 121 ILE cc_start: 0.8506 (mm) cc_final: 0.8298 (mm) REVERT: B 263 LYS cc_start: 0.7158 (mttt) cc_final: 0.6830 (tptt) REVERT: B 397 GLU cc_start: 0.6019 (tt0) cc_final: 0.5596 (tt0) REVERT: B 413 LYS cc_start: 0.8846 (pttt) cc_final: 0.7996 (mmtm) REVERT: B 431 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7505 (tm-30) REVERT: d 30 SER cc_start: 0.9049 (m) cc_final: 0.8803 (t) REVERT: d 68 MET cc_start: 0.7016 (ptm) cc_final: 0.5539 (ppp) REVERT: d 104 LEU cc_start: 0.9507 (mm) cc_final: 0.9275 (mm) REVERT: d 108 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7407 (mt-10) REVERT: d 138 MET cc_start: 0.6435 (mmm) cc_final: 0.5277 (mmm) REVERT: d 165 GLN cc_start: 0.7051 (mt0) cc_final: 0.6673 (mm-40) REVERT: d 190 ASP cc_start: 0.5780 (t70) cc_final: 0.5523 (t70) REVERT: d 280 LYS cc_start: 0.3377 (pptt) cc_final: 0.3063 (mttp) REVERT: d 502 LEU cc_start: 0.8720 (tp) cc_final: 0.8339 (tp) REVERT: D 45 ASP cc_start: 0.8440 (m-30) cc_final: 0.8168 (m-30) REVERT: D 118 THR cc_start: 0.9252 (m) cc_final: 0.8974 (t) REVERT: D 385 MET cc_start: 0.3561 (ppp) cc_final: 0.2846 (pmm) REVERT: D 432 MET cc_start: 0.7533 (ppp) cc_final: 0.7208 (ppp) REVERT: e 142 HIS cc_start: 0.8188 (t70) cc_final: 0.7963 (t70) REVERT: e 146 ILE cc_start: 0.9615 (mt) cc_final: 0.9394 (mt) REVERT: e 429 VAL cc_start: 0.8206 (t) cc_final: 0.7918 (t) REVERT: e 474 GLN cc_start: 0.8162 (tp40) cc_final: 0.7887 (tp40) REVERT: e 481 MET cc_start: 0.9253 (mmm) cc_final: 0.8326 (mmt) REVERT: E 68 ARG cc_start: 0.7017 (ttt-90) cc_final: 0.5850 (ttt-90) REVERT: E 212 MET cc_start: 0.6127 (ttp) cc_final: 0.5810 (ttp) REVERT: E 254 MET cc_start: 0.1903 (mtm) cc_final: 0.1634 (mtm) REVERT: g 277 GLU cc_start: 0.5468 (mt-10) cc_final: 0.5157 (tp30) REVERT: g 494 MET cc_start: 0.6238 (tpp) cc_final: 0.5886 (tpp) REVERT: g 525 ASP cc_start: 0.8447 (p0) cc_final: 0.7659 (p0) REVERT: G 37 THR cc_start: 0.7878 (p) cc_final: 0.7474 (p) REVERT: G 38 CYS cc_start: 0.8823 (m) cc_final: 0.8565 (m) REVERT: G 39 LEU cc_start: 0.7747 (tp) cc_final: 0.7433 (tp) REVERT: G 131 ASP cc_start: 0.8280 (m-30) cc_final: 0.7829 (m-30) REVERT: G 205 ARG cc_start: 0.5655 (tpp-160) cc_final: 0.4159 (ptm160) REVERT: G 234 MET cc_start: 0.3496 (ptp) cc_final: 0.2836 (mpp) REVERT: G 412 LEU cc_start: 0.6172 (tp) cc_final: 0.5970 (tp) REVERT: G 466 ARG cc_start: 0.8723 (mtp180) cc_final: 0.8520 (ttm170) REVERT: q 46 MET cc_start: 0.4142 (tpt) cc_final: 0.3429 (tpt) REVERT: q 98 ASP cc_start: 0.7957 (t0) cc_final: 0.7589 (t0) REVERT: q 161 LYS cc_start: 0.9313 (mttt) cc_final: 0.8994 (mtpt) REVERT: q 287 MET cc_start: 0.4229 (ttm) cc_final: 0.3847 (ttp) REVERT: q 395 ASP cc_start: 0.8048 (p0) cc_final: 0.7575 (p0) REVERT: q 432 SER cc_start: 0.8862 (m) cc_final: 0.8373 (p) REVERT: q 449 ILE cc_start: 0.9368 (mm) cc_final: 0.9116 (mm) REVERT: q 450 LYS cc_start: 0.9040 (mttt) cc_final: 0.8724 (mttt) REVERT: q 546 MET cc_start: 0.4785 (mmm) cc_final: 0.2957 (ptt) REVERT: Q 49 CYS cc_start: 0.8748 (m) cc_final: 0.8496 (m) REVERT: Q 71 MET cc_start: 0.8167 (ppp) cc_final: 0.7682 (ppp) REVERT: Q 92 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8196 (mm-40) REVERT: Q 98 ASP cc_start: 0.6184 (t0) cc_final: 0.5814 (t0) REVERT: Q 102 LEU cc_start: 0.9216 (tp) cc_final: 0.9012 (tt) REVERT: Q 112 ASN cc_start: 0.9013 (t0) cc_final: 0.8603 (t0) REVERT: Q 431 ILE cc_start: 0.9063 (mm) cc_final: 0.8515 (mm) REVERT: z 42 THR cc_start: 0.9660 (p) cc_final: 0.9336 (t) REVERT: z 65 GLU cc_start: 0.6930 (mp0) cc_final: 0.6691 (mp0) REVERT: z 137 LYS cc_start: 0.7684 (pttt) cc_final: 0.6924 (pttt) REVERT: z 151 LEU cc_start: 0.8136 (mt) cc_final: 0.7844 (tp) REVERT: z 167 THR cc_start: 0.8969 (p) cc_final: 0.8642 (p) REVERT: z 199 MET cc_start: 0.6683 (tmm) cc_final: 0.6459 (tmm) REVERT: z 224 MET cc_start: 0.3602 (mmp) cc_final: -0.1078 (ptt) REVERT: z 397 ASP cc_start: 0.8183 (m-30) cc_final: 0.7402 (t70) REVERT: z 422 LEU cc_start: 0.9401 (tp) cc_final: 0.9193 (tt) REVERT: z 525 SER cc_start: 0.8745 (t) cc_final: 0.8426 (t) REVERT: z 530 CYS cc_start: 0.8160 (t) cc_final: 0.7236 (t) REVERT: Z 106 HIS cc_start: 0.7744 (t-90) cc_final: 0.7277 (t-90) REVERT: Z 113 VAL cc_start: 0.9229 (t) cc_final: 0.8386 (p) REVERT: Z 124 ILE cc_start: 0.9102 (tt) cc_final: 0.8790 (tt) REVERT: Z 152 GLN cc_start: 0.8318 (mt0) cc_final: 0.8013 (tt0) REVERT: Z 191 LEU cc_start: 0.8524 (mt) cc_final: 0.8311 (mt) REVERT: Z 193 MET cc_start: 0.7635 (ppp) cc_final: 0.6820 (tmm) REVERT: Z 275 LYS cc_start: 0.6619 (mtmt) cc_final: 0.6362 (mtpt) REVERT: Z 279 ASP cc_start: 0.7425 (m-30) cc_final: 0.7178 (m-30) REVERT: Z 424 ARG cc_start: 0.8277 (mtp-110) cc_final: 0.7937 (mtm180) REVERT: Z 504 GLU cc_start: 0.8490 (tp30) cc_final: 0.8217 (tp30) REVERT: Z 506 ILE cc_start: 0.7951 (mt) cc_final: 0.7472 (mt) REVERT: Z 510 TYR cc_start: 0.8092 (t80) cc_final: 0.7890 (t80) REVERT: h 38 GLU cc_start: 0.8067 (tp30) cc_final: 0.7812 (tp30) REVERT: h 59 LYS cc_start: 0.7662 (tppt) cc_final: 0.7420 (tppt) REVERT: h 187 LEU cc_start: 0.7824 (mt) cc_final: 0.7376 (tt) REVERT: h 216 ASN cc_start: 0.7875 (p0) cc_final: 0.6812 (t0) REVERT: h 307 PHE cc_start: 0.5204 (m-80) cc_final: 0.4964 (m-80) REVERT: h 447 GLU cc_start: 0.8230 (mp0) cc_final: 0.7908 (mp0) REVERT: h 452 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8031 (mm-40) REVERT: h 455 GLU cc_start: 0.7676 (pp20) cc_final: 0.7081 (pp20) REVERT: h 483 PHE cc_start: 0.4853 (m-10) cc_final: 0.4439 (m-80) REVERT: H 126 MET cc_start: 0.7895 (mtp) cc_final: 0.7579 (mtp) REVERT: H 166 MET cc_start: 0.5198 (mmt) cc_final: 0.4549 (mmt) REVERT: H 398 MET cc_start: 0.6235 (mtt) cc_final: 0.6030 (mtp) REVERT: H 418 MET cc_start: 0.7457 (ttt) cc_final: 0.7189 (ttp) REVERT: H 521 ASP cc_start: 0.8622 (p0) cc_final: 0.8381 (p0) outliers start: 1 outliers final: 0 residues processed: 1454 average time/residue: 0.5904 time to fit residues: 1496.0037 Evaluate side-chains 1148 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1148 time to evaluate : 5.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 474 optimal weight: 5.9990 chunk 305 optimal weight: 5.9990 chunk 457 optimal weight: 0.8980 chunk 230 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 487 optimal weight: 5.9990 chunk 522 optimal weight: 3.9990 chunk 378 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 602 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 28 GLN ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 HIS ** a 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 514 HIS A 90 GLN A 209 HIS ** d 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 395 HIS ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 496 HIS D 67 GLN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN e 42 HIS ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 397 GLN E 486 ASN ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 HIS g 286 GLN ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 GLN ** G 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 395 ASN ** G 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 HIS z 83 GLN z 152 GLN ** z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 481 GLN Z 22 ASN Z 69 GLN ** Z 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 231 GLN h 356 GLN ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 GLN H 363 ASN ** H 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.8450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 61671 Z= 0.231 Angle : 0.635 16.877 83183 Z= 0.325 Chirality : 0.045 0.203 10018 Planarity : 0.004 0.066 10682 Dihedral : 4.596 83.328 8441 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.09), residues: 7946 helix: 0.44 (0.08), residues: 3761 sheet: -0.60 (0.20), residues: 682 loop : -1.04 (0.10), residues: 3503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP g 167 HIS 0.010 0.001 HIS E 142 PHE 0.024 0.002 PHE a 139 TYR 0.022 0.002 TYR A 393 ARG 0.018 0.001 ARG q 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1451 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1451 time to evaluate : 5.289 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: a 39 VAL cc_start: 0.9471 (t) cc_final: 0.9264 (t) REVERT: a 51 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8177 (mmmm) REVERT: a 96 ASP cc_start: 0.6592 (m-30) cc_final: 0.6256 (m-30) REVERT: a 108 LEU cc_start: 0.9054 (mm) cc_final: 0.8810 (mm) REVERT: a 114 GLU cc_start: 0.7958 (pp20) cc_final: 0.7553 (pp20) REVERT: a 233 MET cc_start: 0.0805 (mtp) cc_final: 0.0358 (mtp) REVERT: a 297 LEU cc_start: 0.8200 (mp) cc_final: 0.7838 (pp) REVERT: a 455 LEU cc_start: 0.9672 (mm) cc_final: 0.9354 (mm) REVERT: a 460 LYS cc_start: 0.9543 (tttp) cc_final: 0.9037 (ttpp) REVERT: a 471 SER cc_start: 0.9542 (m) cc_final: 0.9219 (t) REVERT: A 44 LEU cc_start: 0.9211 (tt) cc_final: 0.8963 (tt) REVERT: A 73 LEU cc_start: 0.7744 (tp) cc_final: 0.6462 (tt) REVERT: A 88 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7575 (mt0) REVERT: A 107 GLU cc_start: 0.8561 (tp30) cc_final: 0.8172 (tp30) REVERT: A 219 VAL cc_start: 0.3255 (p) cc_final: 0.3035 (p) REVERT: A 233 MET cc_start: 0.4571 (tpp) cc_final: 0.3503 (tpp) REVERT: A 398 MET cc_start: 0.5485 (tpp) cc_final: 0.4915 (tpt) REVERT: A 532 LEU cc_start: 0.9126 (mp) cc_final: 0.8214 (tt) REVERT: b 34 LYS cc_start: 0.9091 (ttpp) cc_final: 0.8823 (ttmm) REVERT: b 36 THR cc_start: 0.9330 (p) cc_final: 0.9046 (t) REVERT: b 45 LEU cc_start: 0.9045 (tp) cc_final: 0.8834 (tp) REVERT: b 47 GLN cc_start: 0.7520 (pp30) cc_final: 0.7052 (pp30) REVERT: b 55 MET cc_start: 0.6363 (mmm) cc_final: 0.5984 (mmm) REVERT: B 42 MET cc_start: 0.7571 (tpt) cc_final: 0.7036 (tpt) REVERT: B 105 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7657 (mm-30) REVERT: B 107 GLU cc_start: 0.8164 (pm20) cc_final: 0.7862 (pm20) REVERT: B 263 LYS cc_start: 0.7214 (mttt) cc_final: 0.6877 (tptt) REVERT: B 413 LYS cc_start: 0.8839 (pttt) cc_final: 0.8015 (mmtt) REVERT: d 80 GLU cc_start: 0.8228 (mp0) cc_final: 0.8026 (pm20) REVERT: d 138 MET cc_start: 0.6454 (mmm) cc_final: 0.6118 (mpp) REVERT: d 165 GLN cc_start: 0.7176 (mt0) cc_final: 0.6721 (mm-40) REVERT: d 192 ASN cc_start: 0.5713 (m-40) cc_final: 0.5418 (t0) REVERT: d 442 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7077 (mm-30) REVERT: d 502 LEU cc_start: 0.8707 (tp) cc_final: 0.8358 (tp) REVERT: D 45 ASP cc_start: 0.8729 (m-30) cc_final: 0.8437 (m-30) REVERT: D 47 MET cc_start: 0.6219 (ppp) cc_final: 0.5601 (ppp) REVERT: D 48 ILE cc_start: 0.6754 (mt) cc_final: 0.6252 (mt) REVERT: D 118 THR cc_start: 0.9141 (m) cc_final: 0.8939 (t) REVERT: D 385 MET cc_start: 0.3677 (ppp) cc_final: 0.3025 (pmm) REVERT: D 432 MET cc_start: 0.7271 (ppp) cc_final: 0.6976 (ppp) REVERT: D 499 GLN cc_start: 0.8336 (mp10) cc_final: 0.7944 (mp10) REVERT: D 528 ARG cc_start: 0.6082 (ttt180) cc_final: 0.5590 (ttt180) REVERT: e 51 ILE cc_start: 0.8957 (mm) cc_final: 0.8343 (mm) REVERT: e 92 SER cc_start: 0.8973 (m) cc_final: 0.8494 (p) REVERT: e 107 LEU cc_start: 0.8468 (mp) cc_final: 0.8214 (mp) REVERT: e 110 SER cc_start: 0.8638 (m) cc_final: 0.8171 (p) REVERT: e 142 HIS cc_start: 0.8242 (t70) cc_final: 0.8035 (t70) REVERT: e 402 LYS cc_start: 0.4547 (mmtm) cc_final: 0.4136 (ptpp) REVERT: e 428 CYS cc_start: 0.7634 (m) cc_final: 0.7425 (m) REVERT: e 429 VAL cc_start: 0.8022 (t) cc_final: 0.7725 (t) REVERT: e 474 GLN cc_start: 0.8068 (tp40) cc_final: 0.7790 (tp40) REVERT: e 481 MET cc_start: 0.9323 (mmm) cc_final: 0.8411 (mmt) REVERT: e 515 LEU cc_start: 0.6225 (pp) cc_final: 0.4961 (mt) REVERT: E 44 LEU cc_start: 0.4326 (pt) cc_final: 0.4033 (pp) REVERT: E 68 ARG cc_start: 0.7262 (ttt-90) cc_final: 0.5991 (ttt-90) REVERT: E 94 MET cc_start: 0.7659 (mmm) cc_final: 0.7393 (mmm) REVERT: E 142 HIS cc_start: 0.7789 (t-90) cc_final: 0.7566 (t-90) REVERT: E 160 LYS cc_start: 0.7915 (tppt) cc_final: 0.7532 (tppt) REVERT: E 212 MET cc_start: 0.6054 (ttp) cc_final: 0.5494 (ttp) REVERT: E 254 MET cc_start: 0.1960 (mtm) cc_final: 0.1701 (mtm) REVERT: g 102 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8285 (mm-30) REVERT: g 135 VAL cc_start: 0.9183 (t) cc_final: 0.8791 (t) REVERT: G 38 CYS cc_start: 0.8879 (m) cc_final: 0.8620 (m) REVERT: G 39 LEU cc_start: 0.7866 (tp) cc_final: 0.7499 (tp) REVERT: G 151 MET cc_start: 0.7367 (mpp) cc_final: 0.6495 (mpp) REVERT: G 205 ARG cc_start: 0.5558 (tpp-160) cc_final: 0.4134 (ptm160) REVERT: G 412 LEU cc_start: 0.6494 (tp) cc_final: 0.5931 (tp) REVERT: q 119 SER cc_start: 0.8698 (m) cc_final: 0.8309 (p) REVERT: q 120 MET cc_start: 0.7155 (tmm) cc_final: 0.6807 (tmm) REVERT: q 161 LYS cc_start: 0.9335 (mttt) cc_final: 0.9050 (mttm) REVERT: q 412 MET cc_start: 0.7367 (ppp) cc_final: 0.6598 (ppp) REVERT: q 432 SER cc_start: 0.8981 (m) cc_final: 0.8481 (p) REVERT: q 450 LYS cc_start: 0.9039 (mttt) cc_final: 0.8755 (mttt) REVERT: q 546 MET cc_start: 0.4416 (mmm) cc_final: 0.3349 (ptt) REVERT: Q 49 CYS cc_start: 0.8741 (m) cc_final: 0.8398 (m) REVERT: Q 92 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8351 (mm-40) REVERT: Q 98 ASP cc_start: 0.6259 (t0) cc_final: 0.5787 (t0) REVERT: Q 109 GLU cc_start: 0.8875 (tp30) cc_final: 0.8672 (tp30) REVERT: Q 112 ASN cc_start: 0.9191 (t0) cc_final: 0.8822 (t0) REVERT: Q 144 GLU cc_start: 0.7856 (pm20) cc_final: 0.7436 (pm20) REVERT: Q 431 ILE cc_start: 0.9183 (mm) cc_final: 0.8647 (mm) REVERT: Q 458 VAL cc_start: 0.9110 (p) cc_final: 0.8832 (p) REVERT: z 65 GLU cc_start: 0.6277 (mp0) cc_final: 0.5631 (mp0) REVERT: z 137 LYS cc_start: 0.7598 (pttt) cc_final: 0.6827 (pttt) REVERT: z 151 LEU cc_start: 0.8201 (mt) cc_final: 0.7953 (tp) REVERT: z 175 THR cc_start: 0.9009 (m) cc_final: 0.8797 (p) REVERT: z 199 MET cc_start: 0.7138 (tmm) cc_final: 0.6839 (tmm) REVERT: z 224 MET cc_start: 0.3588 (mmp) cc_final: -0.1067 (ptt) REVERT: z 397 ASP cc_start: 0.8304 (m-30) cc_final: 0.7623 (t70) REVERT: z 530 CYS cc_start: 0.8553 (t) cc_final: 0.7608 (t) REVERT: Z 9 LYS cc_start: 0.6316 (mmmt) cc_final: 0.5677 (mppt) REVERT: Z 45 MET cc_start: 0.7289 (ttt) cc_final: 0.7083 (ttt) REVERT: Z 106 HIS cc_start: 0.7953 (t-90) cc_final: 0.7336 (t-90) REVERT: Z 124 ILE cc_start: 0.9091 (tt) cc_final: 0.8845 (tt) REVERT: Z 130 MET cc_start: 0.7877 (mmp) cc_final: 0.7674 (tpp) REVERT: Z 152 GLN cc_start: 0.8206 (mt0) cc_final: 0.7956 (tt0) REVERT: Z 191 LEU cc_start: 0.8536 (mt) cc_final: 0.8316 (mt) REVERT: Z 424 ARG cc_start: 0.8386 (mtp-110) cc_final: 0.8145 (mmp80) REVERT: h 59 LYS cc_start: 0.7655 (tppt) cc_final: 0.7443 (tppt) REVERT: h 187 LEU cc_start: 0.7494 (mt) cc_final: 0.6895 (tt) REVERT: h 216 ASN cc_start: 0.7862 (p0) cc_final: 0.6846 (t0) REVERT: h 307 PHE cc_start: 0.5331 (m-80) cc_final: 0.4053 (m-80) REVERT: h 310 ARG cc_start: 0.6375 (mmm160) cc_final: 0.6057 (mtm180) REVERT: h 452 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8195 (mm-40) REVERT: h 455 GLU cc_start: 0.7883 (pp20) cc_final: 0.7333 (pp20) REVERT: h 483 PHE cc_start: 0.4868 (m-10) cc_final: 0.4443 (m-80) REVERT: H 156 GLU cc_start: 0.7067 (mp0) cc_final: 0.6815 (mp0) REVERT: H 521 ASP cc_start: 0.8602 (p0) cc_final: 0.8333 (p0) outliers start: 0 outliers final: 0 residues processed: 1451 average time/residue: 0.5469 time to fit residues: 1365.6996 Evaluate side-chains 1167 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1167 time to evaluate : 5.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 697 optimal weight: 3.9990 chunk 734 optimal weight: 10.0000 chunk 669 optimal weight: 0.9990 chunk 714 optimal weight: 10.0000 chunk 733 optimal weight: 8.9990 chunk 429 optimal weight: 5.9990 chunk 311 optimal weight: 30.0000 chunk 560 optimal weight: 0.9980 chunk 219 optimal weight: 0.5980 chunk 645 optimal weight: 3.9990 chunk 675 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 28 GLN ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 141 ASN a 380 HIS ** a 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 514 HIS A 29 ASN ** d 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 395 HIS d 496 HIS D 67 GLN D 441 GLN e 42 HIS ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN g 21 GLN ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 HIS ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN G 123 GLN ** G 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 HIS ** z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 152 GLN ** z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 430 ASN Z 69 GLN Z 258 GLN Z 312 HIS ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.8580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 61671 Z= 0.170 Angle : 0.597 14.456 83183 Z= 0.302 Chirality : 0.044 0.258 10018 Planarity : 0.003 0.060 10682 Dihedral : 4.391 86.683 8441 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 0.03 % Allowed : 0.43 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.09), residues: 7946 helix: 0.57 (0.08), residues: 3773 sheet: -0.58 (0.20), residues: 675 loop : -1.01 (0.10), residues: 3498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 275 HIS 0.013 0.001 HIS d 473 PHE 0.026 0.001 PHE H 459 TYR 0.018 0.001 TYR Z 355 ARG 0.011 0.000 ARG h 361 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1433 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1431 time to evaluate : 5.314 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: a 108 LEU cc_start: 0.8990 (mm) cc_final: 0.8626 (mm) REVERT: a 114 GLU cc_start: 0.7942 (pp20) cc_final: 0.7484 (pp20) REVERT: a 297 LEU cc_start: 0.8358 (mp) cc_final: 0.7928 (pp) REVERT: a 455 LEU cc_start: 0.9659 (mm) cc_final: 0.9342 (mm) REVERT: a 460 LYS cc_start: 0.9526 (tttp) cc_final: 0.8977 (ttmm) REVERT: a 471 SER cc_start: 0.9534 (m) cc_final: 0.9146 (t) REVERT: A 44 LEU cc_start: 0.9196 (tt) cc_final: 0.8810 (tt) REVERT: A 73 LEU cc_start: 0.7609 (tp) cc_final: 0.6323 (tt) REVERT: A 88 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7570 (mt0) REVERT: A 107 GLU cc_start: 0.8451 (tp30) cc_final: 0.8120 (tp30) REVERT: A 219 VAL cc_start: 0.3167 (p) cc_final: 0.2924 (p) REVERT: A 233 MET cc_start: 0.4694 (tpp) cc_final: 0.3657 (tpp) REVERT: A 385 ILE cc_start: 0.5574 (mt) cc_final: 0.4714 (mt) REVERT: A 398 MET cc_start: 0.5096 (tpp) cc_final: 0.4463 (tpt) REVERT: A 532 LEU cc_start: 0.9063 (mp) cc_final: 0.8183 (tt) REVERT: b 27 ILE cc_start: 0.8724 (mt) cc_final: 0.8393 (mm) REVERT: b 31 ASP cc_start: 0.8153 (m-30) cc_final: 0.7848 (m-30) REVERT: b 34 LYS cc_start: 0.9015 (ttpp) cc_final: 0.8655 (ttmm) REVERT: b 36 THR cc_start: 0.9315 (p) cc_final: 0.8989 (t) REVERT: b 47 GLN cc_start: 0.7757 (pp30) cc_final: 0.7245 (pp30) REVERT: b 55 MET cc_start: 0.6455 (mmm) cc_final: 0.5986 (mmm) REVERT: b 241 ASP cc_start: 0.3180 (p0) cc_final: 0.2974 (p0) REVERT: b 426 LYS cc_start: 0.8594 (mmtp) cc_final: 0.8045 (mptt) REVERT: b 490 SER cc_start: 0.8987 (p) cc_final: 0.8645 (m) REVERT: B 42 MET cc_start: 0.7435 (tpt) cc_final: 0.7048 (tpt) REVERT: B 105 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7361 (mm-30) REVERT: B 107 GLU cc_start: 0.8255 (pm20) cc_final: 0.7948 (pm20) REVERT: B 263 LYS cc_start: 0.7193 (mttt) cc_final: 0.6866 (tptt) REVERT: B 413 LYS cc_start: 0.8718 (pttt) cc_final: 0.7985 (mmtt) REVERT: d 68 MET cc_start: 0.6639 (ptm) cc_final: 0.6414 (ppp) REVERT: d 138 MET cc_start: 0.6536 (mmm) cc_final: 0.5368 (mmm) REVERT: d 165 GLN cc_start: 0.7197 (mt0) cc_final: 0.6663 (mm-40) REVERT: d 190 ASP cc_start: 0.5721 (t70) cc_final: 0.5413 (t70) REVERT: d 442 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7638 (mm-30) REVERT: d 502 LEU cc_start: 0.8715 (tp) cc_final: 0.8397 (tp) REVERT: d 518 ILE cc_start: 0.9397 (mm) cc_final: 0.9132 (mm) REVERT: D 45 ASP cc_start: 0.8671 (m-30) cc_final: 0.8354 (m-30) REVERT: D 47 MET cc_start: 0.6538 (ppp) cc_final: 0.6034 (ppp) REVERT: D 68 MET cc_start: 0.6533 (ptm) cc_final: 0.6281 (ppp) REVERT: D 499 GLN cc_start: 0.8468 (mp10) cc_final: 0.8151 (mp10) REVERT: D 528 ARG cc_start: 0.6198 (ttt180) cc_final: 0.5628 (ttt180) REVERT: e 51 ILE cc_start: 0.8919 (mm) cc_final: 0.8318 (mm) REVERT: e 92 SER cc_start: 0.8919 (m) cc_final: 0.8479 (p) REVERT: e 142 HIS cc_start: 0.8135 (t70) cc_final: 0.7921 (t70) REVERT: e 389 LYS cc_start: 0.5633 (pptt) cc_final: 0.5246 (mmmt) REVERT: e 402 LYS cc_start: 0.4514 (mmtm) cc_final: 0.4128 (ptpp) REVERT: e 428 CYS cc_start: 0.7573 (m) cc_final: 0.7295 (m) REVERT: e 429 VAL cc_start: 0.8159 (t) cc_final: 0.7877 (t) REVERT: e 474 GLN cc_start: 0.7993 (tp40) cc_final: 0.7737 (tp40) REVERT: e 481 MET cc_start: 0.9292 (mmm) cc_final: 0.8868 (tpt) REVERT: e 515 LEU cc_start: 0.6128 (pp) cc_final: 0.4958 (mt) REVERT: E 68 ARG cc_start: 0.7038 (ttt-90) cc_final: 0.5970 (ttt-90) REVERT: E 104 LEU cc_start: 0.7172 (mt) cc_final: 0.6808 (mt) REVERT: E 160 LYS cc_start: 0.7822 (tppt) cc_final: 0.7424 (tppt) REVERT: E 212 MET cc_start: 0.6195 (ttp) cc_final: 0.5712 (ttp) REVERT: E 254 MET cc_start: 0.1984 (mtm) cc_final: 0.1748 (mtm) REVERT: E 486 ASN cc_start: 0.8007 (m-40) cc_final: 0.6321 (m-40) REVERT: g 18 ARG cc_start: 0.6581 (ptt-90) cc_final: 0.5981 (mmp80) REVERT: g 102 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8192 (mm-30) REVERT: g 106 GLN cc_start: 0.7786 (tp40) cc_final: 0.7507 (tp40) REVERT: g 135 VAL cc_start: 0.9064 (t) cc_final: 0.8755 (t) REVERT: G 25 ILE cc_start: 0.9015 (mm) cc_final: 0.8797 (mm) REVERT: G 38 CYS cc_start: 0.8823 (m) cc_final: 0.8532 (m) REVERT: G 39 LEU cc_start: 0.7875 (tp) cc_final: 0.7540 (tp) REVERT: G 48 LEU cc_start: 0.8138 (mp) cc_final: 0.7897 (mp) REVERT: G 151 MET cc_start: 0.7498 (mpp) cc_final: 0.6739 (mpp) REVERT: G 234 MET cc_start: 0.2906 (ptp) cc_final: 0.2052 (mpp) REVERT: G 406 VAL cc_start: 0.7822 (t) cc_final: 0.7612 (t) REVERT: G 421 MET cc_start: 0.7471 (ttt) cc_final: 0.6946 (ttt) REVERT: G 471 LEU cc_start: 0.8254 (tp) cc_final: 0.7799 (tp) REVERT: G 494 MET cc_start: 0.6054 (tpt) cc_final: 0.5829 (tpt) REVERT: q 41 MET cc_start: 0.7498 (tmm) cc_final: 0.7201 (tmm) REVERT: q 119 SER cc_start: 0.8759 (m) cc_final: 0.8436 (p) REVERT: q 120 MET cc_start: 0.7007 (tmm) cc_final: 0.6611 (tmm) REVERT: q 145 MET cc_start: 0.8724 (mmp) cc_final: 0.8516 (mmm) REVERT: q 412 MET cc_start: 0.7083 (ppp) cc_final: 0.6528 (ppp) REVERT: q 432 SER cc_start: 0.9009 (m) cc_final: 0.8535 (p) REVERT: q 449 ILE cc_start: 0.9186 (mm) cc_final: 0.8709 (tp) REVERT: q 450 LYS cc_start: 0.8956 (mttt) cc_final: 0.8658 (mttt) REVERT: q 546 MET cc_start: 0.4740 (mmm) cc_final: 0.3834 (ptp) REVERT: Q 49 CYS cc_start: 0.8654 (m) cc_final: 0.8355 (m) REVERT: Q 66 ASN cc_start: 0.8069 (m-40) cc_final: 0.7664 (t0) REVERT: Q 92 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8434 (mm-40) REVERT: Q 98 ASP cc_start: 0.6098 (t0) cc_final: 0.5741 (t0) REVERT: Q 106 LEU cc_start: 0.9215 (mm) cc_final: 0.9013 (mm) REVERT: Q 112 ASN cc_start: 0.9109 (t0) cc_final: 0.8752 (t0) REVERT: Q 144 GLU cc_start: 0.7926 (pm20) cc_final: 0.7495 (pm20) REVERT: Q 431 ILE cc_start: 0.9149 (mm) cc_final: 0.8607 (mm) REVERT: Q 458 VAL cc_start: 0.9122 (p) cc_final: 0.8858 (p) REVERT: z 137 LYS cc_start: 0.7539 (pttt) cc_final: 0.6871 (pttt) REVERT: z 151 LEU cc_start: 0.8242 (mt) cc_final: 0.7967 (tp) REVERT: z 152 GLN cc_start: 0.8649 (mt0) cc_final: 0.8223 (mt0) REVERT: z 175 THR cc_start: 0.9020 (m) cc_final: 0.8807 (p) REVERT: z 199 MET cc_start: 0.6870 (tmm) cc_final: 0.6630 (tmm) REVERT: z 224 MET cc_start: 0.3591 (mmp) cc_final: -0.1032 (ptt) REVERT: z 327 ARG cc_start: 0.6357 (mtt180) cc_final: 0.6143 (mtt180) REVERT: z 397 ASP cc_start: 0.8218 (m-30) cc_final: 0.7535 (t70) REVERT: z 530 CYS cc_start: 0.8618 (t) cc_final: 0.7770 (t) REVERT: Z 106 HIS cc_start: 0.7737 (t-90) cc_final: 0.7160 (t-90) REVERT: Z 431 MET cc_start: 0.4060 (mmm) cc_final: 0.3693 (mmp) REVERT: h 59 LYS cc_start: 0.7679 (tppt) cc_final: 0.7345 (tppt) REVERT: h 187 LEU cc_start: 0.7494 (mt) cc_final: 0.6992 (pp) REVERT: h 216 ASN cc_start: 0.7835 (p0) cc_final: 0.6874 (t0) REVERT: h 307 PHE cc_start: 0.5372 (m-80) cc_final: 0.4964 (m-80) REVERT: h 355 MET cc_start: 0.3695 (tpt) cc_final: 0.3243 (tpt) REVERT: h 452 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8207 (mm-40) REVERT: h 455 GLU cc_start: 0.7925 (pp20) cc_final: 0.7510 (pp20) REVERT: h 483 PHE cc_start: 0.4989 (m-10) cc_final: 0.4625 (m-80) REVERT: H 156 GLU cc_start: 0.6897 (mp0) cc_final: 0.6645 (mp0) REVERT: H 490 ASP cc_start: 0.6527 (t70) cc_final: 0.6243 (p0) REVERT: H 498 GLU cc_start: 0.8273 (mp0) cc_final: 0.7268 (mp0) REVERT: H 521 ASP cc_start: 0.8541 (p0) cc_final: 0.8245 (p0) REVERT: H 523 THR cc_start: 0.6920 (p) cc_final: 0.6714 (p) outliers start: 2 outliers final: 0 residues processed: 1432 average time/residue: 0.5500 time to fit residues: 1359.8315 Evaluate side-chains 1180 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1180 time to evaluate : 5.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 711 optimal weight: 0.5980 chunk 468 optimal weight: 10.0000 chunk 755 optimal weight: 5.9990 chunk 460 optimal weight: 2.9990 chunk 358 optimal weight: 10.0000 chunk 524 optimal weight: 1.9990 chunk 792 optimal weight: 3.9990 chunk 728 optimal weight: 9.9990 chunk 630 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 487 optimal weight: 0.0170 overall best weight: 1.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 28 GLN ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 HIS a 417 ASN a 514 HIS A 90 GLN ** d 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 395 HIS d 496 HIS D 67 GLN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN e 42 HIS ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 HIS ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 GLN ** G 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 446 GLN ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 HIS ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 69 GLN ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.8781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 61671 Z= 0.177 Angle : 0.601 13.854 83183 Z= 0.304 Chirality : 0.044 0.230 10018 Planarity : 0.003 0.058 10682 Dihedral : 4.331 87.898 8441 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.09), residues: 7946 helix: 0.59 (0.09), residues: 3764 sheet: -0.56 (0.20), residues: 684 loop : -1.00 (0.10), residues: 3498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 275 HIS 0.011 0.001 HIS d 395 PHE 0.026 0.001 PHE B 218 TYR 0.015 0.001 TYR Q 496 ARG 0.011 0.000 ARG q 440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1421 time to evaluate : 5.243 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 108 LEU cc_start: 0.9061 (mm) cc_final: 0.8788 (mm) REVERT: a 114 GLU cc_start: 0.7963 (pp20) cc_final: 0.7448 (pp20) REVERT: a 117 LYS cc_start: 0.8795 (mmtm) cc_final: 0.8583 (mmmt) REVERT: a 146 THR cc_start: 0.6030 (m) cc_final: 0.5647 (p) REVERT: a 297 LEU cc_start: 0.8477 (mp) cc_final: 0.8027 (pp) REVERT: a 445 GLN cc_start: 0.7217 (mp10) cc_final: 0.7000 (mp10) REVERT: a 455 LEU cc_start: 0.9651 (mm) cc_final: 0.9325 (mm) REVERT: a 460 LYS cc_start: 0.9526 (tttp) cc_final: 0.8981 (ttmm) REVERT: a 471 SER cc_start: 0.9500 (m) cc_final: 0.9119 (t) REVERT: A 44 LEU cc_start: 0.9203 (tt) cc_final: 0.8822 (tt) REVERT: A 73 LEU cc_start: 0.7665 (tp) cc_final: 0.6440 (tt) REVERT: A 107 GLU cc_start: 0.8422 (tp30) cc_final: 0.8139 (tp30) REVERT: A 219 VAL cc_start: 0.3107 (p) cc_final: 0.2856 (p) REVERT: A 233 MET cc_start: 0.4566 (tpp) cc_final: 0.3451 (tpp) REVERT: A 532 LEU cc_start: 0.9034 (mp) cc_final: 0.8196 (tt) REVERT: b 23 PHE cc_start: 0.7140 (m-10) cc_final: 0.6939 (m-10) REVERT: b 34 LYS cc_start: 0.8978 (ttpp) cc_final: 0.8627 (ttmt) REVERT: b 36 THR cc_start: 0.9244 (p) cc_final: 0.9034 (t) REVERT: b 47 GLN cc_start: 0.7852 (pp30) cc_final: 0.7293 (pp30) REVERT: b 55 MET cc_start: 0.6538 (mmm) cc_final: 0.6285 (mmm) REVERT: b 101 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7877 (mm-30) REVERT: b 409 MET cc_start: 0.8331 (mmp) cc_final: 0.8067 (mmp) REVERT: b 490 SER cc_start: 0.9177 (p) cc_final: 0.8846 (m) REVERT: B 42 MET cc_start: 0.7480 (tpt) cc_final: 0.7040 (tpt) REVERT: B 105 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7389 (mm-30) REVERT: B 107 GLU cc_start: 0.8366 (pm20) cc_final: 0.8029 (pm20) REVERT: B 263 LYS cc_start: 0.7192 (mttt) cc_final: 0.6859 (tptt) REVERT: B 413 LYS cc_start: 0.8889 (pttt) cc_final: 0.7862 (mmtt) REVERT: d 47 MET cc_start: 0.7919 (tmm) cc_final: 0.7493 (tmm) REVERT: d 68 MET cc_start: 0.6486 (ptm) cc_final: 0.6203 (ppp) REVERT: d 77 MET cc_start: 0.7774 (mtp) cc_final: 0.7451 (mtp) REVERT: d 80 GLU cc_start: 0.8273 (pm20) cc_final: 0.8005 (pm20) REVERT: d 138 MET cc_start: 0.6672 (mmm) cc_final: 0.6148 (mpp) REVERT: d 165 GLN cc_start: 0.7198 (mt0) cc_final: 0.6647 (mm-40) REVERT: d 190 ASP cc_start: 0.5687 (t70) cc_final: 0.5379 (t70) REVERT: d 442 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7539 (mm-30) REVERT: d 461 ASN cc_start: 0.8641 (t0) cc_final: 0.8428 (t0) REVERT: d 502 LEU cc_start: 0.8721 (tp) cc_final: 0.8385 (tp) REVERT: D 45 ASP cc_start: 0.8679 (m-30) cc_final: 0.8358 (m-30) REVERT: D 47 MET cc_start: 0.6552 (ppp) cc_final: 0.5842 (ppp) REVERT: D 68 MET cc_start: 0.6775 (ptm) cc_final: 0.6448 (ppp) REVERT: D 71 LEU cc_start: 0.6563 (mt) cc_final: 0.6292 (tt) REVERT: D 499 GLN cc_start: 0.8545 (mp10) cc_final: 0.8258 (mp10) REVERT: D 528 ARG cc_start: 0.6220 (ttt180) cc_final: 0.5608 (ttt180) REVERT: e 51 ILE cc_start: 0.8844 (mm) cc_final: 0.8144 (mm) REVERT: e 92 SER cc_start: 0.9024 (m) cc_final: 0.8701 (p) REVERT: e 142 HIS cc_start: 0.8120 (t70) cc_final: 0.7915 (t70) REVERT: e 389 LYS cc_start: 0.5621 (pptt) cc_final: 0.5241 (mmmt) REVERT: e 402 LYS cc_start: 0.4650 (mmtm) cc_final: 0.4404 (ptpp) REVERT: e 428 CYS cc_start: 0.7544 (m) cc_final: 0.7276 (m) REVERT: e 429 VAL cc_start: 0.8170 (t) cc_final: 0.7882 (t) REVERT: e 474 GLN cc_start: 0.7988 (tp40) cc_final: 0.7760 (tp40) REVERT: e 515 LEU cc_start: 0.6084 (pp) cc_final: 0.5036 (mt) REVERT: E 104 LEU cc_start: 0.7274 (mt) cc_final: 0.6902 (mt) REVERT: E 212 MET cc_start: 0.6219 (ttp) cc_final: 0.5698 (ttp) REVERT: E 254 MET cc_start: 0.1578 (mtm) cc_final: 0.1339 (mtm) REVERT: E 526 PHE cc_start: 0.6591 (m-80) cc_final: 0.6308 (m-80) REVERT: g 33 ASP cc_start: 0.7191 (t70) cc_final: 0.6794 (m-30) REVERT: g 89 VAL cc_start: 0.8915 (m) cc_final: 0.8677 (t) REVERT: g 106 GLN cc_start: 0.7812 (tp40) cc_final: 0.7524 (tp40) REVERT: g 135 VAL cc_start: 0.9082 (t) cc_final: 0.8758 (t) REVERT: G 25 ILE cc_start: 0.8910 (mm) cc_final: 0.8681 (mm) REVERT: G 38 CYS cc_start: 0.8836 (m) cc_final: 0.8611 (m) REVERT: G 39 LEU cc_start: 0.7736 (tp) cc_final: 0.7437 (tp) REVERT: G 151 MET cc_start: 0.7442 (mpp) cc_final: 0.6429 (mpp) REVERT: G 234 MET cc_start: 0.3032 (ptp) cc_final: 0.2100 (mpp) REVERT: G 421 MET cc_start: 0.7472 (ttt) cc_final: 0.6779 (ttt) REVERT: G 471 LEU cc_start: 0.8244 (tp) cc_final: 0.7893 (tp) REVERT: G 507 GLN cc_start: 0.8237 (pt0) cc_final: 0.7954 (pt0) REVERT: q 41 MET cc_start: 0.7459 (tmm) cc_final: 0.7125 (tmm) REVERT: q 110 LEU cc_start: 0.9262 (mm) cc_final: 0.8926 (mm) REVERT: q 119 SER cc_start: 0.8744 (m) cc_final: 0.8447 (p) REVERT: q 126 GLU cc_start: 0.7558 (tp30) cc_final: 0.7205 (tp30) REVERT: q 213 MET cc_start: 0.3289 (mmt) cc_final: 0.0485 (ppp) REVERT: q 287 MET cc_start: 0.3038 (ttm) cc_final: 0.2498 (tpp) REVERT: q 395 ASP cc_start: 0.7903 (p0) cc_final: 0.6991 (p0) REVERT: q 412 MET cc_start: 0.6731 (ppp) cc_final: 0.6107 (ppp) REVERT: q 432 SER cc_start: 0.9030 (m) cc_final: 0.8435 (p) REVERT: q 450 LYS cc_start: 0.8859 (mttt) cc_final: 0.8524 (mttt) REVERT: q 511 ASP cc_start: 0.7993 (t70) cc_final: 0.7739 (t0) REVERT: q 546 MET cc_start: 0.4792 (mmm) cc_final: 0.3860 (ptp) REVERT: Q 49 CYS cc_start: 0.8598 (m) cc_final: 0.8260 (m) REVERT: Q 66 ASN cc_start: 0.8109 (m-40) cc_final: 0.7704 (t0) REVERT: Q 92 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8481 (mm-40) REVERT: Q 98 ASP cc_start: 0.6108 (t0) cc_final: 0.5693 (t0) REVERT: Q 112 ASN cc_start: 0.9244 (t0) cc_final: 0.8775 (t0) REVERT: Q 144 GLU cc_start: 0.7810 (pm20) cc_final: 0.7380 (pm20) REVERT: Q 431 ILE cc_start: 0.9173 (mm) cc_final: 0.8661 (mm) REVERT: Q 546 MET cc_start: -0.1151 (pmm) cc_final: -0.1697 (pmm) REVERT: z 45 MET cc_start: 0.7132 (ttp) cc_final: 0.6866 (ttp) REVERT: z 137 LYS cc_start: 0.7507 (pttt) cc_final: 0.6971 (pttt) REVERT: z 151 LEU cc_start: 0.8233 (mt) cc_final: 0.7954 (tp) REVERT: z 152 GLN cc_start: 0.8693 (mt0) cc_final: 0.8312 (mt0) REVERT: z 175 THR cc_start: 0.9037 (m) cc_final: 0.8837 (p) REVERT: z 199 MET cc_start: 0.7010 (tmm) cc_final: 0.6562 (tmm) REVERT: z 224 MET cc_start: 0.3466 (mmp) cc_final: -0.1011 (ptt) REVERT: z 364 PHE cc_start: 0.6718 (m-10) cc_final: 0.6515 (m-10) REVERT: z 431 MET cc_start: 0.5799 (ptt) cc_final: 0.3904 (tpp) REVERT: z 449 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7534 (mt-10) REVERT: z 530 CYS cc_start: 0.8701 (t) cc_final: 0.7773 (t) REVERT: Z 48 ASP cc_start: 0.7513 (p0) cc_final: 0.7308 (p0) REVERT: Z 106 HIS cc_start: 0.7949 (t-90) cc_final: 0.7353 (t-90) REVERT: Z 191 LEU cc_start: 0.8291 (mt) cc_final: 0.8090 (mt) REVERT: Z 275 LYS cc_start: 0.6567 (mtmt) cc_final: 0.6354 (pttm) REVERT: Z 431 MET cc_start: 0.4405 (mmm) cc_final: 0.3968 (mmp) REVERT: h 59 LYS cc_start: 0.7732 (tppt) cc_final: 0.7478 (tppt) REVERT: h 163 ARG cc_start: 0.6158 (mmp80) cc_final: 0.4431 (tpp-160) REVERT: h 169 LYS cc_start: 0.5523 (mtpt) cc_final: 0.4919 (mmmt) REVERT: h 187 LEU cc_start: 0.7635 (mt) cc_final: 0.7121 (pp) REVERT: h 216 ASN cc_start: 0.7767 (p0) cc_final: 0.6971 (t0) REVERT: h 276 GLN cc_start: 0.6523 (pt0) cc_final: 0.6191 (pm20) REVERT: h 307 PHE cc_start: 0.5401 (m-80) cc_final: 0.4823 (m-80) REVERT: h 355 MET cc_start: 0.3638 (tpt) cc_final: 0.3071 (tpt) REVERT: h 452 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8182 (mm-40) REVERT: h 455 GLU cc_start: 0.7911 (pp20) cc_final: 0.7500 (pp20) REVERT: h 483 PHE cc_start: 0.4716 (m-10) cc_final: 0.4276 (m-80) REVERT: H 156 GLU cc_start: 0.6974 (mp0) cc_final: 0.6675 (mp0) REVERT: H 181 MET cc_start: 0.2671 (mtm) cc_final: 0.2451 (mtm) REVERT: H 418 MET cc_start: 0.7406 (ttt) cc_final: 0.7099 (mmm) REVERT: H 446 LEU cc_start: 0.9351 (mm) cc_final: 0.9101 (mm) REVERT: H 498 GLU cc_start: 0.8236 (mp0) cc_final: 0.7331 (mp0) REVERT: H 523 THR cc_start: 0.6830 (p) cc_final: 0.6628 (p) outliers start: 0 outliers final: 0 residues processed: 1421 average time/residue: 0.5377 time to fit residues: 1327.1365 Evaluate side-chains 1178 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1178 time to evaluate : 5.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 386 optimal weight: 0.0670 chunk 500 optimal weight: 0.3980 chunk 671 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 581 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 631 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 648 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 28 GLN ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 HIS a 514 HIS A 29 ASN d 59 ASN ** d 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 496 HIS D 67 GLN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN D 457 ASN ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 537 GLN E 486 ASN ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 HIS ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 GLN ** G 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 GLN ** q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 HIS ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 104 GLN ** z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 312 HIS ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.222519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.204152 restraints weight = 149585.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.201000 restraints weight = 187635.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.198364 restraints weight = 169714.324| |-----------------------------------------------------------------------------| r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.8886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 61671 Z= 0.154 Angle : 0.580 12.026 83183 Z= 0.291 Chirality : 0.043 0.197 10018 Planarity : 0.003 0.057 10682 Dihedral : 4.201 88.344 8441 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.09), residues: 7946 helix: 0.71 (0.09), residues: 3761 sheet: -0.48 (0.20), residues: 672 loop : -0.96 (0.10), residues: 3513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 275 HIS 0.011 0.001 HIS d 395 PHE 0.026 0.001 PHE H 492 TYR 0.019 0.001 TYR Z 510 ARG 0.008 0.000 ARG h 451 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19735.88 seconds wall clock time: 344 minutes 11.76 seconds (20651.76 seconds total)