Starting phenix.real_space_refine on Sat Dec 9 18:11:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gw5_9541/12_2023/5gw5_9541.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gw5_9541/12_2023/5gw5_9541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gw5_9541/12_2023/5gw5_9541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gw5_9541/12_2023/5gw5_9541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gw5_9541/12_2023/5gw5_9541.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gw5_9541/12_2023/5gw5_9541.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.028 sd= 0.165 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 320 5.16 5 C 40466 2.51 5 N 11186 2.21 5 O 12572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 493": "OD1" <-> "OD2" Residue "z TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 64544 Number of models: 1 Model: "" Number of chains: 16 Chain: "a" Number of atoms: 4103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4103 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 11, 'TRANS': 531} Chain: "A" Number of atoms: 4103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4103 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 11, 'TRANS': 531} Chain: "b" Number of atoms: 3930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3930 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 10, 'TRANS': 506} Chain: "B" Number of atoms: 3930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3930 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 10, 'TRANS': 506} Chain: "d" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3985 Classifications: {'peptide': 521} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain: "D" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3985 Classifications: {'peptide': 521} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain: "e" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4068 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "E" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4068 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "g" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3982 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 19, 'TRANS': 498} Chain: "G" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3982 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 19, 'TRANS': 498} Chain: "h" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3969 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 12, 'TRANS': 506} Chain: "H" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3969 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 12, 'TRANS': 506} Chain: "q" Number of atoms: 4125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4125 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 19, 'TRANS': 523} Chain: "Q" Number of atoms: 4125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4125 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 19, 'TRANS': 523} Chain: "z" Number of atoms: 4110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4110 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 16, 'TRANS': 517} Chain: "Z" Number of atoms: 4110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4110 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 16, 'TRANS': 517} Time building chain proxies: 25.17, per 1000 atoms: 0.39 Number of scatterers: 64544 At special positions: 0 Unit cell: (195.064, 221.424, 180.566, 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 320 16.00 O 12572 8.00 N 11186 7.00 C 40466 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: 17.98 Conformation dependent library (CDL) restraints added in 9.4 seconds 16828 Ramachandran restraints generated. 8414 Oldfield, 0 Emsley, 8414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15724 Finding SS restraints... Secondary structure from input PDB file: 325 helices and 95 sheets defined 55.1% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.48 Creating SS restraints... Processing helix chain 'a' and resid 22 through 41 removed outlier: 3.512A pdb=" N VAL a 30 " --> pdb=" O ARG a 26 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL a 39 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL a 40 " --> pdb=" O VAL a 36 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 73 Processing helix chain 'a' and resid 77 through 94 removed outlier: 4.224A pdb=" N LEU a 83 " --> pdb=" O ALA a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 118 removed outlier: 3.675A pdb=" N VAL a 101 " --> pdb=" O GLY a 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE a 103 " --> pdb=" O THR a 99 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU a 114 " --> pdb=" O LYS a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 144 removed outlier: 3.590A pdb=" N GLU a 142 " --> pdb=" O ARG a 138 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU a 144 " --> pdb=" O ILE a 140 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 164 Processing helix chain 'a' and resid 167 through 171 Processing helix chain 'a' and resid 172 through 186 removed outlier: 3.868A pdb=" N ASN a 178 " --> pdb=" O ASP a 174 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET a 179 " --> pdb=" O PHE a 175 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU a 184 " --> pdb=" O VAL a 180 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA a 186 " --> pdb=" O ASP a 182 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 216 Processing helix chain 'a' and resid 267 through 290 removed outlier: 3.921A pdb=" N GLU a 271 " --> pdb=" O PRO a 267 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL a 281 " --> pdb=" O GLU a 277 " (cutoff:3.500A) Processing helix chain 'a' and resid 304 through 313 removed outlier: 3.596A pdb=" N GLU a 309 " --> pdb=" O LEU a 305 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE a 310 " --> pdb=" O CYS a 306 " (cutoff:3.500A) Processing helix chain 'a' and resid 322 through 334 removed outlier: 4.179A pdb=" N ARG a 328 " --> pdb=" O GLU a 324 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 415 removed outlier: 4.206A pdb=" N VAL a 408 " --> pdb=" O ASP a 404 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER a 415 " --> pdb=" O ARG a 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 423 through 437 Processing helix chain 'a' and resid 438 through 440 No H-bonds generated for 'chain 'a' and resid 438 through 440' Processing helix chain 'a' and resid 443 through 454 removed outlier: 3.676A pdb=" N ALA a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) Processing helix chain 'a' and resid 456 through 465 removed outlier: 3.523A pdb=" N ALA a 463 " --> pdb=" O PRO a 459 " (cutoff:3.500A) Processing helix chain 'a' and resid 469 through 488 removed outlier: 3.855A pdb=" N ALA a 475 " --> pdb=" O SER a 471 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET a 486 " --> pdb=" O ALA a 482 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA a 487 " --> pdb=" O ALA a 483 " (cutoff:3.500A) Processing helix chain 'a' and resid 512 through 516 Processing helix chain 'a' and resid 521 through 540 removed outlier: 3.502A pdb=" N GLU a 533 " --> pdb=" O LYS a 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 38 removed outlier: 3.575A pdb=" N VAL A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.920A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 118 removed outlier: 3.515A pdb=" N ILE A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 144 removed outlier: 3.926A pdb=" N GLU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 172 through 187 removed outlier: 3.872A pdb=" N ASN A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 183 " --> pdb=" O MET A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 266 through 290 removed outlier: 3.932A pdb=" N GLU A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.627A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 removed outlier: 3.997A pdb=" N ARG A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 415 removed outlier: 3.835A pdb=" N VAL A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 438 through 440 No H-bonds generated for 'chain 'A' and resid 438 through 440' Processing helix chain 'A' and resid 443 through 454 removed outlier: 3.915A pdb=" N ALA A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 465 Processing helix chain 'A' and resid 469 through 488 removed outlier: 3.564A pdb=" N LEU A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 516 Processing helix chain 'A' and resid 521 through 540 Processing helix chain 'b' and resid 14 through 34 removed outlier: 3.757A pdb=" N VAL b 33 " --> pdb=" O VAL b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 59 through 67 Processing helix chain 'b' and resid 71 through 88 removed outlier: 3.799A pdb=" N LEU b 77 " --> pdb=" O ALA b 73 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL b 88 " --> pdb=" O GLN b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 111 removed outlier: 3.804A pdb=" N LYS b 108 " --> pdb=" O ARG b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 138 Processing helix chain 'b' and resid 145 through 161 Processing helix chain 'b' and resid 164 through 168 Processing helix chain 'b' and resid 169 through 185 removed outlier: 3.840A pdb=" N GLU b 175 " --> pdb=" O ASP b 171 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU b 184 " --> pdb=" O ALA b 180 " (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 278 removed outlier: 3.798A pdb=" N ALA b 264 " --> pdb=" O GLN b 260 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU b 265 " --> pdb=" O LEU b 261 " (cutoff:3.500A) Processing helix chain 'b' and resid 291 through 301 Processing helix chain 'b' and resid 310 through 321 Processing helix chain 'b' and resid 373 through 397 removed outlier: 4.087A pdb=" N ARG b 382 " --> pdb=" O ASP b 378 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR b 395 " --> pdb=" O LEU b 391 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS b 396 " --> pdb=" O SER b 392 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 419 Processing helix chain 'b' and resid 423 through 449 removed outlier: 4.125A pdb=" N LEU b 428 " --> pdb=" O GLY b 424 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA b 429 " --> pdb=" O LYS b 425 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU b 440 " --> pdb=" O ALA b 436 " (cutoff:3.500A) Proline residue: b 441 - end of helix Processing helix chain 'b' and resid 451 through 465 removed outlier: 3.513A pdb=" N ASN b 465 " --> pdb=" O SER b 461 " (cutoff:3.500A) Processing helix chain 'b' and resid 491 through 510 removed outlier: 3.618A pdb=" N LEU b 508 " --> pdb=" O ALA b 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 34 removed outlier: 3.517A pdb=" N LEU B 20 " --> pdb=" O GLU B 16 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 71 through 88 removed outlier: 3.624A pdb=" N LEU B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 109 removed outlier: 3.502A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 139 Processing helix chain 'B' and resid 145 through 162 removed outlier: 3.559A pdb=" N GLU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.653A pdb=" N GLN B 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 183 removed outlier: 3.944A pdb=" N GLU B 175 " --> pdb=" O ASP B 171 " (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 278 removed outlier: 4.073A pdb=" N LEU B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 373 through 397 removed outlier: 3.863A pdb=" N ARG B 382 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 393 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 419 Processing helix chain 'B' and resid 423 through 449 removed outlier: 4.144A pdb=" N LEU B 428 " --> pdb=" O GLY B 424 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix Processing helix chain 'B' and resid 451 through 465 removed outlier: 3.576A pdb=" N SER B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 Processing helix chain 'B' and resid 491 through 511 removed outlier: 3.664A pdb=" N VAL B 511 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 36 removed outlier: 3.549A pdb=" N ARG d 21 " --> pdb=" O PRO d 17 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA d 32 " --> pdb=" O ALA d 28 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA d 34 " --> pdb=" O SER d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 60 through 68 Processing helix chain 'd' and resid 72 through 89 removed outlier: 3.957A pdb=" N LEU d 78 " --> pdb=" O VAL d 74 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU d 80 " --> pdb=" O ARG d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 113 removed outlier: 3.912A pdb=" N VAL d 97 " --> pdb=" O THR d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 116 through 139 removed outlier: 3.577A pdb=" N ASP d 133 " --> pdb=" O LYS d 129 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET d 138 " --> pdb=" O ILE d 134 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 158 removed outlier: 3.989A pdb=" N LEU d 150 " --> pdb=" O ASP d 146 " (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 182 Proline residue: d 172 - end of helix removed outlier: 3.947A pdb=" N ILE d 181 " --> pdb=" O SER d 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 256 through 281 Processing helix chain 'd' and resid 298 through 308 Processing helix chain 'd' and resid 317 through 328 removed outlier: 3.844A pdb=" N GLU d 322 " --> pdb=" O ARG d 318 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE d 323 " --> pdb=" O GLU d 319 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS d 326 " --> pdb=" O GLU d 322 " (cutoff:3.500A) Processing helix chain 'd' and resid 335 through 339 Processing helix chain 'd' and resid 383 through 407 removed outlier: 3.688A pdb=" N ILE d 387 " --> pdb=" O ASN d 383 " (cutoff:3.500A) Processing helix chain 'd' and resid 415 through 429 removed outlier: 3.527A pdb=" N ILE d 419 " --> pdb=" O GLY d 415 " (cutoff:3.500A) Processing helix chain 'd' and resid 434 through 447 removed outlier: 4.110A pdb=" N PHE d 438 " --> pdb=" O GLY d 434 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE d 439 " --> pdb=" O VAL d 435 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP d 440 " --> pdb=" O GLN d 436 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN d 441 " --> pdb=" O ALA d 437 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU d 442 " --> pdb=" O PHE d 438 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA d 444 " --> pdb=" O TRP d 440 " (cutoff:3.500A) Processing helix chain 'd' and resid 448 through 458 Processing helix chain 'd' and resid 461 through 476 removed outlier: 3.844A pdb=" N GLU d 474 " --> pdb=" O ARG d 470 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN d 475 " --> pdb=" O SER d 471 " (cutoff:3.500A) Processing helix chain 'd' and resid 501 through 520 removed outlier: 3.504A pdb=" N ILE d 508 " --> pdb=" O SER d 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 36 removed outlier: 3.546A pdb=" N ARG D 21 " --> pdb=" O PRO D 17 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 35 " --> pdb=" O VAL D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 72 through 89 removed outlier: 4.019A pdb=" N LEU D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 113 removed outlier: 3.626A pdb=" N VAL D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 138 Processing helix chain 'D' and resid 146 through 158 removed outlier: 3.860A pdb=" N LEU D 150 " --> pdb=" O ASP D 146 " (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 182 Proline residue: D 172 - end of helix removed outlier: 4.074A pdb=" N ILE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 281 removed outlier: 3.726A pdb=" N MET D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP D 261 " --> pdb=" O TYR D 257 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA D 281 " --> pdb=" O LYS D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 317 through 328 removed outlier: 3.652A pdb=" N PHE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 407 removed outlier: 3.597A pdb=" N ILE D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 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 433 through 434 No H-bonds generated for 'chain 'D' and resid 433 through 434' Processing helix chain 'D' and resid 435 through 447 removed outlier: 3.602A pdb=" N ILE D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.536A pdb=" N GLU D 474 " --> pdb=" O ARG D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 520 Processing helix chain 'e' and resid 43 through 63 removed outlier: 3.689A pdb=" N LYS e 47 " --> pdb=" O GLY e 43 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS e 48 " --> pdb=" O LEU e 44 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE e 51 " --> pdb=" O LYS e 47 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE e 60 " --> pdb=" O SER e 56 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE e 61 " --> pdb=" O VAL e 57 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR e 63 " --> pdb=" O SER e 59 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 94 Processing helix chain 'e' and resid 98 through 115 removed outlier: 3.540A pdb=" N LEU e 104 " --> pdb=" O ILE e 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 118 through 138 removed outlier: 3.954A pdb=" N VAL e 123 " --> pdb=" O THR e 119 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL e 124 " --> pdb=" O THR e 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 164 removed outlier: 3.780A pdb=" N THR e 164 " --> pdb=" O LYS e 160 " (cutoff:3.500A) Processing helix chain 'e' and resid 172 through 188 removed outlier: 3.544A pdb=" N PHE e 176 " --> pdb=" O ASN e 172 " (cutoff:3.500A) removed outlier: 3.530A 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: 3.657A pdb=" N PHE e 200 " --> pdb=" O ASP e 196 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU e 202 " --> pdb=" O ASP e 198 " (cutoff:3.500A) removed outlier: 3.533A 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 Processing helix chain 'e' and resid 291 through 317 removed outlier: 3.521A pdb=" N TYR e 295 " --> pdb=" O SER e 291 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN e 303 " --> pdb=" O GLN e 299 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS e 307 " --> pdb=" O GLN e 303 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL e 313 " --> pdb=" O MET e 309 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS e 314 " --> pdb=" O ILE e 310 " (cutoff:3.500A) Processing helix chain 'e' and resid 328 through 338 Processing helix chain 'e' and resid 347 through 358 Processing helix chain 'e' and resid 412 through 436 removed outlier: 3.507A pdb=" N ASN e 432 " --> pdb=" O CYS e 428 " (cutoff:3.500A) Processing helix chain 'e' and resid 444 through 462 removed outlier: 3.737A pdb=" N VAL e 448 " --> pdb=" O GLY e 444 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR e 449 " --> pdb=" O ALA e 445 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP e 459 " --> pdb=" O SER e 455 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS e 460 " --> pdb=" O GLU e 456 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN e 461 " --> pdb=" O GLU e 457 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG e 462 " --> pdb=" O ALA e 458 " (cutoff:3.500A) Processing helix chain 'e' and resid 464 through 477 removed outlier: 3.596A pdb=" N ALA e 468 " --> pdb=" O ILE e 464 " (cutoff:3.500A) Processing helix chain 'e' and resid 477 through 487 Processing helix chain 'e' and resid 490 through 502 removed outlier: 3.549A pdb=" N GLN e 502 " --> pdb=" O LEU e 498 " (cutoff:3.500A) Processing helix chain 'e' and resid 512 through 516 removed outlier: 4.644A pdb=" N LEU e 515 " --> pdb=" O VAL e 512 " (cutoff:3.500A) Processing helix chain 'e' and resid 521 through 526 removed outlier: 3.752A pdb=" N LEU e 525 " --> pdb=" O ASP e 521 " (cutoff:3.500A) Processing helix chain 'e' and resid 531 through 550 Processing helix chain 'E' and resid 43 through 63 removed outlier: 3.579A pdb=" N LYS E 47 " --> pdb=" O GLY E 43 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS E 48 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER E 49 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE E 61 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR E 63 " --> pdb=" O SER E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 94 Processing helix chain 'E' and resid 98 through 115 removed outlier: 3.713A pdb=" N ASP E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 139 removed outlier: 3.889A pdb=" N VAL E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 165 removed outlier: 3.536A pdb=" N SER E 159 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 188 Processing helix chain 'E' and resid 191 through 195 removed outlier: 3.558A pdb=" N LYS E 195 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 212 removed outlier: 3.626A pdb=" N PHE E 200 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.656A 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 Processing helix chain 'E' and resid 291 through 317 removed outlier: 3.599A pdb=" N TYR E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR E 300 " --> pdb=" O GLN E 296 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP E 312 " --> pdb=" O GLU E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 338 removed outlier: 3.685A pdb=" N LEU E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN E 337 " --> pdb=" O HIS E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 358 Processing helix chain 'E' and resid 365 through 369 removed outlier: 3.544A pdb=" N LEU E 369 " --> pdb=" O PHE E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 436 Processing helix chain 'E' and resid 445 through 462 removed outlier: 4.342A pdb=" N ASP E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS E 460 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG E 462 " --> pdb=" O ALA E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 477 removed outlier: 3.917A pdb=" N TYR E 467 " --> pdb=" O GLY E 463 " (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 531 through 550 removed outlier: 3.513A pdb=" N THR E 542 " --> pdb=" O ILE E 538 " (cutoff:3.500A) Processing helix chain 'g' and resid 17 through 36 removed outlier: 4.100A pdb=" N GLN g 21 " --> pdb=" O GLY g 17 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL g 34 " --> pdb=" O ALA g 30 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE g 35 " --> pdb=" O VAL g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 39 No H-bonds generated for 'chain 'g' and resid 37 through 39' Processing helix chain 'g' and resid 60 through 67 removed outlier: 3.560A pdb=" N LEU g 65 " --> pdb=" O GLY g 61 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU g 67 " --> pdb=" O ALA g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 72 through 89 removed outlier: 3.606A pdb=" N GLU g 87 " --> pdb=" O ARG g 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU g 88 " --> pdb=" O THR g 84 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 107 removed outlier: 3.528A pdb=" N ILE g 97 " --> pdb=" O THR g 93 " (cutoff:3.500A) removed outlier: 4.019A 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: 3.660A pdb=" N LYS g 127 " --> pdb=" O GLN g 123 " (cutoff:3.500A) Processing helix chain 'g' and resid 147 through 160 removed outlier: 3.554A pdb=" N LYS g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA g 157 " --> pdb=" O LYS g 153 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER g 158 " --> pdb=" O LEU g 154 " (cutoff:3.500A) Processing helix chain 'g' and resid 162 through 166 removed outlier: 4.205A pdb=" N HIS g 166 " --> pdb=" O TYR g 163 " (cutoff:3.500A) Processing helix chain 'g' and resid 167 through 183 removed outlier: 3.528A pdb=" N ALA g 178 " --> pdb=" O LEU g 174 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR g 181 " --> pdb=" O ASP g 177 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL g 182 " --> pdb=" O ALA g 178 " (cutoff:3.500A) Processing helix chain 'g' and resid 213 through 217 Processing helix chain 'g' and resid 265 through 267 No H-bonds generated for 'chain 'g' and resid 265 through 267' Processing helix chain 'g' and resid 268 through 289 removed outlier: 3.927A pdb=" N ILE g 272 " --> pdb=" O ASP g 268 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE g 275 " --> pdb=" O ARG g 271 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE g 287 " --> pdb=" O MET g 283 " (cutoff:3.500A) Processing helix chain 'g' and resid 302 through 311 Processing helix chain 'g' and resid 321 through 333 removed outlier: 3.509A pdb=" N ARG g 327 " --> pdb=" O SER g 323 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG g 330 " --> pdb=" O ASN g 326 " (cutoff:3.500A) Processing helix chain 'g' and resid 339 through 343 removed outlier: 3.815A pdb=" N LEU g 343 " --> pdb=" O VAL g 340 " (cutoff:3.500A) Processing helix chain 'g' and resid 385 through 408 Processing helix chain 'g' and resid 417 through 431 removed outlier: 3.517A pdb=" N SER g 424 " --> pdb=" O GLU g 420 " (cutoff:3.500A) Processing helix chain 'g' and resid 432 through 434 No H-bonds generated for 'chain 'g' and resid 432 through 434' Processing helix chain 'g' and resid 438 through 450 removed outlier: 3.599A pdb=" N ALA g 444 " --> pdb=" O TRP g 440 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL g 445 " --> pdb=" O PRO g 441 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA g 446 " --> pdb=" O TYR g 442 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU g 450 " --> pdb=" O ALA g 446 " (cutoff:3.500A) Processing helix chain 'g' and resid 450 through 461 Processing helix chain 'g' and resid 463 through 478 Processing helix chain 'g' and resid 503 through 522 Processing helix chain 'G' and resid 18 through 36 removed outlier: 3.800A pdb=" N ILE G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 60 through 68 removed outlier: 3.712A pdb=" N GLU G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 89 removed outlier: 3.712A pdb=" N LYS G 76 " --> pdb=" O HIS G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 107 removed outlier: 3.685A pdb=" N VAL G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 117 through 140 Processing helix chain 'G' and resid 147 through 160 removed outlier: 3.532A pdb=" N LYS G 153 " --> pdb=" O ALA G 149 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA G 157 " --> pdb=" O LYS G 153 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER G 158 " --> pdb=" O LEU G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 166 removed outlier: 4.213A pdb=" N HIS G 166 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 183 removed outlier: 3.513A pdb=" N ALA G 178 " --> pdb=" O LEU G 174 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR G 181 " --> pdb=" O ASP G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 217 Processing helix chain 'G' and resid 265 through 267 No H-bonds generated for 'chain 'G' and resid 265 through 267' Processing helix chain 'G' and resid 268 through 289 removed outlier: 3.535A pdb=" N ILE G 272 " --> pdb=" O ASP G 268 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU G 277 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE G 287 " --> pdb=" O MET G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 311 Processing helix chain 'G' and resid 321 through 333 removed outlier: 3.738A pdb=" N ARG G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL G 331 " --> pdb=" O ARG G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 343 removed outlier: 3.574A pdb=" N LEU G 343 " --> pdb=" O VAL G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 408 Processing helix chain 'G' and resid 417 through 433 removed outlier: 3.689A pdb=" N LYS G 432 " --> pdb=" O ALA G 428 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN G 433 " --> pdb=" O GLU G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 450 removed outlier: 3.628A pdb=" N ALA G 444 " --> pdb=" O TRP G 440 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL G 445 " --> pdb=" O PRO G 441 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA G 446 " --> pdb=" O TYR G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 461 Processing helix chain 'G' and resid 463 through 477 Processing helix chain 'G' and resid 503 through 522 Processing helix chain 'h' and resid 22 through 41 Processing helix chain 'h' and resid 65 through 74 removed outlier: 3.506A pdb=" N LEU h 72 " --> pdb=" O THR h 68 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP h 74 " --> pdb=" O LEU h 70 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 94 Processing helix chain 'h' and resid 97 through 111 removed outlier: 3.877A pdb=" N THR h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET h 109 " --> pdb=" O ALA h 105 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 119 Processing helix chain 'h' and resid 121 through 144 Processing helix chain 'h' and resid 153 through 166 removed outlier: 3.669A pdb=" N LEU h 158 " --> pdb=" O GLY h 154 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR h 164 " --> pdb=" O ARG h 160 " (cutoff:3.500A) Processing helix chain 'h' and resid 174 through 188 removed outlier: 3.611A pdb=" N PHE h 178 " --> pdb=" O ASN h 174 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS h 180 " --> pdb=" O ASP h 176 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET h 181 " --> pdb=" O PHE h 177 " (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: 3.867A pdb=" N SER h 212 " --> pdb=" O MET h 209 " (cutoff:3.500A) Processing helix chain 'h' and resid 264 through 289 removed outlier: 4.308A pdb=" N GLN h 268 " --> pdb=" O VAL h 264 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA h 269 " --> pdb=" O GLU h 265 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS h 281 " --> pdb=" O LEU h 277 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL h 285 " --> pdb=" O LYS h 281 " (cutoff:3.500A) Processing helix chain 'h' and resid 300 through 310 Processing helix chain 'h' and resid 319 through 331 removed outlier: 3.722A pdb=" N ARG h 325 " --> pdb=" O ASP h 321 " (cutoff:3.500A) Processing helix chain 'h' and resid 342 through 346 Processing helix chain 'h' and resid 382 through 406 removed outlier: 3.621A pdb=" N GLN h 405 " --> pdb=" O LYS h 401 " (cutoff:3.500A) Processing helix chain 'h' and resid 414 through 431 removed outlier: 4.111A pdb=" N LYS h 429 " --> pdb=" O ARG h 425 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR h 430 " --> pdb=" O ASP h 426 " (cutoff:3.500A) Processing helix chain 'h' and resid 433 through 446 removed outlier: 4.253A pdb=" N MET h 437 " --> pdb=" O GLY h 433 " (cutoff:3.500A) Processing helix chain 'h' and resid 447 through 458 removed outlier: 3.507A pdb=" N ALA h 457 " --> pdb=" O LEU h 453 " (cutoff:3.500A) Processing helix chain 'h' and resid 460 through 473 removed outlier: 3.590A pdb=" N LEU h 465 " --> pdb=" O ALA h 461 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA h 471 " --> pdb=" O LYS h 467 " (cutoff:3.500A) removed outlier: 3.814A 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 519 Processing helix chain 'H' and resid 22 through 41 removed outlier: 3.607A pdb=" N ILE H 26 " --> pdb=" O GLY H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 74 removed outlier: 3.880A pdb=" N ASP H 74 " --> pdb=" O LEU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 94 removed outlier: 3.787A pdb=" N LEU H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 112 removed outlier: 3.899A pdb=" N THR H 102 " --> pdb=" O THR H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 119 Processing helix chain 'H' and resid 121 through 144 removed outlier: 3.576A pdb=" N GLU H 138 " --> pdb=" O SER H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 166 removed outlier: 3.804A pdb=" N LEU H 158 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR H 164 " --> pdb=" O ARG H 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA H 165 " --> pdb=" O CYS H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 188 removed outlier: 3.847A pdb=" N LYS H 180 " --> pdb=" O ASP H 176 " (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: 3.744A pdb=" N SER H 212 " --> pdb=" O MET H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 289 removed outlier: 3.625A pdb=" N ILE H 278 " --> pdb=" O GLU H 274 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS H 281 " --> pdb=" O LEU H 277 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU H 286 " --> pdb=" O LEU H 282 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY H 289 " --> pdb=" O VAL H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 310 removed outlier: 3.703A pdb=" N ARG H 310 " --> pdb=" O PHE H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 331 removed outlier: 3.657A pdb=" N ARG H 325 " --> pdb=" O ASP H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 346 Processing helix chain 'H' and resid 382 through 406 removed outlier: 3.557A pdb=" N ILE H 399 " --> pdb=" O ASP H 395 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU H 404 " --> pdb=" O VAL H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 431 removed outlier: 3.519A pdb=" N LEU H 424 " --> pdb=" O VAL H 420 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG H 425 " --> pdb=" O SER H 421 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP H 426 " --> pdb=" O LYS H 422 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS H 429 " --> pdb=" O ARG H 425 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR H 430 " --> pdb=" O ASP H 426 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE H 431 " --> pdb=" O TYR H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 446 removed outlier: 3.995A pdb=" N MET H 437 " --> pdb=" O GLY H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 457 Processing helix chain 'H' and resid 460 through 472 removed outlier: 3.541A pdb=" N LEU H 465 " --> pdb=" O ALA H 461 " (cutoff:3.500A) Processing helix chain 'H' and resid 473 through 475 No H-bonds generated for 'chain 'H' and resid 473 through 475' Processing helix chain 'H' and resid 491 through 495 Processing helix chain 'H' and resid 500 through 519 Processing helix chain 'q' and resid 22 through 25 Processing helix chain 'q' and resid 26 through 44 removed outlier: 3.762A pdb=" N LEU q 38 " --> pdb=" O ALA q 34 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET q 41 " --> pdb=" O GLU q 37 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS q 42 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR q 44 " --> pdb=" O GLN q 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 67 through 75 removed outlier: 3.537A pdb=" N MET q 71 " --> pdb=" O ASP q 67 " (cutoff:3.500A) Processing helix chain 'q' and resid 79 through 94 removed outlier: 4.247A pdb=" N LEU q 85 " --> pdb=" O ALA q 81 " (cutoff:3.500A) Processing helix chain 'q' and resid 99 through 121 removed outlier: 3.653A pdb=" N MET q 104 " --> pdb=" O THR q 100 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU q 111 " --> pdb=" O ALA q 107 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS q 116 " --> pdb=" O ASN q 112 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU q 117 " --> pdb=" O VAL q 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 123 through 145 removed outlier: 3.797A pdb=" N ASP q 143 " --> pdb=" O LEU q 139 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU q 144 " --> pdb=" O LYS q 140 " (cutoff:3.500A) Processing helix chain 'q' and resid 155 through 168 removed outlier: 3.645A pdb=" N MET q 162 " --> pdb=" O GLU q 158 " (cutoff:3.500A) Proline residue: q 165 - end of helix Processing helix chain 'q' and resid 174 through 190 removed outlier: 3.909A pdb=" N GLU q 180 " --> pdb=" O ASP q 176 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU q 181 " --> pdb=" O ILE q 177 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA q 185 " --> pdb=" O LEU q 181 " (cutoff:3.500A) Processing helix chain 'q' and resid 203 through 205 No H-bonds generated for 'chain 'q' and resid 203 through 205' Processing helix chain 'q' and resid 216 through 220 Processing helix chain 'q' and resid 269 through 294 removed outlier: 3.544A pdb=" N MET q 273 " --> pdb=" O ASN q 269 " (cutoff:3.500A) Processing helix chain 'q' and resid 306 through 316 removed outlier: 3.575A pdb=" N LEU q 313 " --> pdb=" O ALA q 309 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG q 315 " --> pdb=" O HIS q 311 " (cutoff:3.500A) Processing helix chain 'q' and resid 325 through 337 removed outlier: 3.612A pdb=" N ARG q 331 " --> pdb=" O PHE q 327 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG q 334 " --> pdb=" O ARG q 330 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL q 335 " --> pdb=" O ARG q 331 " (cutoff:3.500A) Processing helix chain 'q' and resid 390 through 410 Processing helix chain 'q' and resid 424 through 441 removed outlier: 3.543A pdb=" N ARG q 440 " --> pdb=" O LYS q 436 " (cutoff:3.500A) Processing helix chain 'q' and resid 444 through 455 removed outlier: 4.087A 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 Proline residue: q 476 - end of helix Processing helix chain 'q' and resid 511 through 516 removed outlier: 4.180A pdb=" N GLU q 515 " --> pdb=" O ASP q 511 " (cutoff:3.500A) Processing helix chain 'q' and resid 521 through 539 Processing helix chain 'Q' and resid 22 through 25 Processing helix chain 'Q' and resid 26 through 44 removed outlier: 3.687A pdb=" N LEU Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 75 removed outlier: 4.031A pdb=" N MET Q 71 " --> pdb=" O ASP Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 96 removed outlier: 3.624A pdb=" N LEU Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP Q 95 " --> pdb=" O GLN Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 121 removed outlier: 3.517A pdb=" N VAL Q 103 " --> pdb=" O GLY Q 99 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET Q 104 " --> pdb=" O THR Q 100 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU Q 111 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU Q 115 " --> pdb=" O LEU Q 111 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS Q 116 " --> pdb=" O ASN Q 112 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU Q 117 " --> pdb=" O VAL Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 145 removed outlier: 3.656A pdb=" N GLU Q 144 " --> pdb=" O LYS Q 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 155 through 168 removed outlier: 3.798A pdb=" N MET Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) Proline residue: Q 165 - end of helix removed outlier: 3.541A pdb=" N SER Q 168 " --> pdb=" O LYS Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 190 removed outlier: 3.815A pdb=" N GLU Q 180 " --> pdb=" O ASP Q 176 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU Q 181 " --> pdb=" O ILE Q 177 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU Q 184 " --> pdb=" O GLU Q 180 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA Q 185 " --> pdb=" O LEU Q 181 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS Q 188 " --> pdb=" O GLU Q 184 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL Q 189 " --> pdb=" O ALA Q 185 " (cutoff:3.500A) Processing helix chain 'Q' and resid 203 through 205 No H-bonds generated for 'chain 'Q' and resid 203 through 205' Processing helix chain 'Q' and resid 216 through 220 Processing helix chain 'Q' and resid 269 through 294 removed outlier: 3.506A pdb=" N GLU Q 290 " --> pdb=" O ALA Q 286 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 316 removed outlier: 3.570A pdb=" N ARG Q 315 " --> pdb=" O HIS Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 325 through 333 removed outlier: 3.541A pdb=" N LEU Q 329 " --> pdb=" O SER Q 325 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG Q 331 " --> pdb=" O PHE Q 327 " (cutoff:3.500A) Processing helix chain 'Q' and resid 390 through 409 Processing helix chain 'Q' and resid 410 through 412 No H-bonds generated for 'chain 'Q' and resid 410 through 412' Processing helix chain 'Q' and resid 424 through 441 removed outlier: 3.814A pdb=" N ILE Q 428 " --> pdb=" O GLY Q 424 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU Q 429 " --> pdb=" O ALA Q 425 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER Q 432 " --> pdb=" O ILE Q 428 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG Q 440 " --> pdb=" O LYS Q 436 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 455 removed outlier: 4.284A 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 473 through 482 removed outlier: 3.730A pdb=" N HIS Q 482 " --> pdb=" O LEU Q 478 " (cutoff:3.500A) Processing helix chain 'Q' and resid 511 through 516 removed outlier: 4.198A pdb=" N GLU Q 515 " --> pdb=" O ASP Q 511 " (cutoff:3.500A) Processing helix chain 'Q' and resid 521 through 540 removed outlier: 3.512A pdb=" N PHE Q 526 " --> pdb=" O ALA Q 522 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 34 Processing helix chain 'z' and resid 58 through 66 removed outlier: 3.506A pdb=" N GLU z 65 " --> pdb=" O VAL z 61 " (cutoff:3.500A) Processing helix chain 'z' and resid 70 through 87 removed outlier: 3.500A pdb=" N LEU z 75 " --> pdb=" O PRO z 71 " (cutoff:3.500A) Processing helix chain 'z' and resid 90 through 110 removed outlier: 3.848A pdb=" N PHE z 108 " --> pdb=" O GLN z 104 " (cutoff:3.500A) Processing helix chain 'z' and resid 114 through 137 Processing helix chain 'z' and resid 146 through 162 removed outlier: 3.675A pdb=" N GLN z 152 " --> pdb=" O GLU z 148 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR z 160 " --> pdb=" O SER z 156 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS z 161 " --> pdb=" O SER z 157 " (cutoff:3.500A) Processing helix chain 'z' and resid 166 through 182 Proline residue: z 172 - end of helix removed outlier: 3.556A pdb=" N VAL z 181 " --> pdb=" O ALA z 177 " (cutoff:3.500A) Processing helix chain 'z' and resid 190 through 192 No H-bonds generated for 'chain 'z' and resid 190 through 192' Processing helix chain 'z' and resid 203 through 207 Processing helix chain 'z' and resid 255 through 284 removed outlier: 4.148A pdb=" N PHE z 269 " --> pdb=" O SER z 265 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL z 270 " --> pdb=" O GLU z 266 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS z 273 " --> pdb=" O PHE z 269 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS z 281 " --> pdb=" O ILE z 277 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN z 282 " --> pdb=" O ILE z 278 " (cutoff:3.500A) Processing helix chain 'z' and resid 302 through 312 Processing helix chain 'z' and resid 321 through 332 removed outlier: 3.695A pdb=" N GLN z 329 " --> pdb=" O MET z 325 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU z 330 " --> pdb=" O GLU z 326 " (cutoff:3.500A) Processing helix chain 'z' and resid 339 through 343 Processing helix chain 'z' and resid 384 through 408 removed outlier: 3.728A pdb=" N LEU z 388 " --> pdb=" O THR z 384 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG z 400 " --> pdb=" O ARG z 396 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL z 405 " --> pdb=" O ALA z 401 " (cutoff:3.500A) Processing helix chain 'z' and resid 416 through 434 removed outlier: 3.910A pdb=" N MET z 431 " --> pdb=" O ARG z 427 " (cutoff:3.500A) Processing helix chain 'z' and resid 439 through 451 removed outlier: 4.369A pdb=" N GLY z 443 " --> pdb=" O LYS z 439 " (cutoff:3.500A) Processing helix chain 'z' and resid 452 through 463 removed outlier: 3.624A pdb=" N VAL z 459 " --> pdb=" O PRO z 455 " (cutoff:3.500A) Processing helix chain 'z' and resid 465 through 483 Processing helix chain 'z' and resid 500 through 505 Processing helix chain 'z' and resid 510 through 529 removed outlier: 3.504A pdb=" N ILE z 517 " --> pdb=" O LEU z 513 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR z 518 " --> pdb=" O ARG z 514 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 34 removed outlier: 3.515A pdb=" N VAL Z 32 " --> pdb=" O GLY Z 28 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 66 removed outlier: 3.591A pdb=" N THR Z 64 " --> pdb=" O LYS Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 70 through 87 Processing helix chain 'Z' and resid 90 through 111 removed outlier: 3.769A pdb=" N PHE Z 108 " --> pdb=" O GLN Z 104 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 137 Processing helix chain 'Z' and resid 146 through 159 Processing helix chain 'Z' and resid 164 through 182 removed outlier: 4.062A pdb=" N GLU Z 168 " --> pdb=" O ALA Z 164 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL Z 169 " --> pdb=" O ASP Z 165 " (cutoff:3.500A) Proline residue: Z 172 - end of helix removed outlier: 3.512A 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: 3.527A pdb=" N ARG Z 259 " --> pdb=" O SER Z 255 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP Z 260 " --> pdb=" O ALA Z 256 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE Z 269 " --> pdb=" O SER Z 265 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL Z 270 " --> pdb=" O GLU Z 266 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS Z 273 " --> pdb=" O PHE Z 269 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS Z 281 " --> pdb=" O ILE Z 277 " (cutoff:3.500A) Processing helix chain 'Z' and resid 302 through 312 Processing helix chain 'Z' and resid 321 through 333 removed outlier: 3.658A pdb=" N GLU Z 326 " --> pdb=" O ARG Z 322 " (cutoff:3.500A) Processing helix chain 'Z' and resid 339 through 343 Processing helix chain 'Z' and resid 384 through 408 removed outlier: 3.673A pdb=" N LEU Z 388 " --> pdb=" O THR Z 384 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL Z 405 " --> pdb=" O ALA Z 401 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 434 removed outlier: 3.766A pdb=" N MET Z 431 " --> pdb=" O ARG Z 427 " (cutoff:3.500A) Processing helix chain 'Z' and resid 439 through 451 removed outlier: 4.353A pdb=" N GLY Z 443 " --> pdb=" O LYS Z 439 " (cutoff:3.500A) Processing helix chain 'Z' and resid 452 through 463 removed outlier: 3.632A pdb=" N VAL Z 459 " --> pdb=" O PRO Z 455 " (cutoff:3.500A) Processing helix chain 'Z' and resid 465 through 483 Processing helix chain 'Z' and resid 500 through 505 Processing helix chain 'Z' and resid 510 through 529 Processing sheet with id=AA1, first strand: chain 'a' and resid 18 through 21 removed outlier: 3.613A pdb=" N SER d 58 " --> pdb=" O LYS d 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 60 through 63 removed outlier: 3.518A pdb=" N THR a 63 " --> pdb=" O LYS a 51 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS a 51 " --> pdb=" O THR a 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 145 through 146 removed outlier: 4.835A pdb=" N SER a 145 " --> pdb=" O VAL a 418 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL a 418 " --> pdb=" O SER a 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 204 through 208 Processing sheet with id=AA5, first strand: chain 'a' and resid 223 through 224 removed outlier: 3.811A pdb=" N CYS a 371 " --> pdb=" O ALA a 364 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL a 361 " --> pdb=" O ILE a 237 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE a 237 " --> pdb=" O VAL a 361 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 316 through 318 removed outlier: 3.623A pdb=" N ILE a 244 " --> pdb=" O GLY a 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 500 through 503 removed outlier: 3.505A pdb=" N VAL a 510 " --> pdb=" O GLY a 501 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.364A pdb=" N ILE A 541 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N MET D 47 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR A 543 " --> pdb=" O MET D 47 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N LYS D 49 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 545 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER D 58 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 60 through 63 removed outlier: 3.577A pdb=" N LYS A 51 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL G 527 " --> pdb=" O MET A 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 204 through 207 removed outlier: 6.566A pdb=" N ASN A 204 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU A 387 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU A 206 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 222 through 224 removed outlier: 6.247A pdb=" N THR A 377 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS A 358 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 361 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 237 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 244 through 247 Processing sheet with id=AB4, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AB5, first strand: chain 'A' and resid 500 through 503 removed outlier: 3.744A pdb=" N VAL A 510 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 55 through 57 removed outlier: 3.577A pdb=" N THR b 57 " --> pdb=" O LYS b 44 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS b 44 " --> pdb=" O THR b 57 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ASP b 43 " --> pdb=" O ASP d 523 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N ALA d 525 " --> pdb=" O ASP b 43 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU b 45 " --> pdb=" O ALA d 525 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 140 through 141 Processing sheet with id=AB8, first strand: chain 'b' and resid 193 through 199 removed outlier: 6.233A pdb=" N GLN b 194 " --> pdb=" O ILE b 367 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU b 369 " --> pdb=" O GLN b 194 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE b 196 " --> pdb=" O LEU b 369 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY b 371 " --> pdb=" O ILE b 196 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE b 198 " --> pdb=" O GLY b 371 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 213 through 214 removed outlier: 6.227A pdb=" N GLU b 339 " --> pdb=" O LYS b 230 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS b 230 " --> pdb=" O GLU b 339 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP b 341 " --> pdb=" O ASN b 228 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR b 283 " --> pdb=" O ASN b 228 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LYS b 230 " --> pdb=" O THR b 283 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE b 285 " --> pdb=" O LYS b 230 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU b 232 " --> pdb=" O ILE b 285 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE b 284 " --> pdb=" O ILE b 306 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 471 through 472 removed outlier: 3.770A pdb=" N ALA b 480 " --> pdb=" O GLY b 471 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 511 through 516 removed outlier: 6.857A pdb=" N ASP e 71 " --> pdb=" O VAL b 511 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASN b 513 " --> pdb=" O ASP e 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 11 through 13 Processing sheet with id=AC4, first strand: chain 'B' and resid 55 through 57 removed outlier: 3.613A pdb=" N THR B 57 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B 44 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ASP B 43 " --> pdb=" O ASP D 523 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N ALA D 525 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B 45 " --> pdb=" O ALA D 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AC6, first strand: chain 'B' and resid 193 through 199 removed outlier: 6.139A pdb=" N GLN B 194 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU B 369 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 196 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY B 371 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 198 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 213 through 214 removed outlier: 6.202A pdb=" N CYS B 359 " --> pdb=" O CYS B 340 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N CYS B 340 " --> pdb=" O CYS B 359 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP B 341 " --> pdb=" O ASN B 228 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 231 through 234 Processing sheet with id=AC9, first strand: chain 'B' and resid 248 through 249 Processing sheet with id=AD1, first strand: chain 'B' and resid 471 through 472 removed outlier: 3.772A pdb=" N ALA B 480 " --> pdb=" O GLY B 471 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 194 through 200 removed outlier: 6.354A pdb=" N ARG d 195 " --> pdb=" O VAL d 377 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE d 379 " --> pdb=" O ARG d 195 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL d 197 " --> pdb=" O ILE d 379 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N GLY d 381 " --> pdb=" O VAL d 197 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS d 199 " --> pdb=" O GLY d 381 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU d 208 " --> pdb=" O VAL d 378 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 213 through 214 removed outlier: 3.603A pdb=" N LEU d 349 " --> pdb=" O THR d 364 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP d 348 " --> pdb=" O LYS d 231 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 311 through 316 removed outlier: 3.888A pdb=" N ASP d 315 " --> pdb=" O ILE d 288 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU d 236 " --> pdb=" O ILE d 333 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 410 through 412 Processing sheet with id=AD6, first strand: chain 'd' and resid 480 through 483 Processing sheet with id=AD7, first strand: chain 'D' and resid 194 through 200 removed outlier: 5.963A pdb=" N ARG D 195 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE D 379 " --> pdb=" O ARG D 195 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL D 197 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLY D 381 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS D 199 " --> pdb=" O GLY D 381 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER D 376 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 208 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 228 through 232 removed outlier: 6.443A pdb=" N ARG D 228 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU D 351 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU D 230 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU D 349 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 349 " --> pdb=" O THR D 364 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU D 351 " --> pdb=" O ARG D 362 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 311 through 316 removed outlier: 3.528A pdb=" N ASP D 315 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY D 235 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N ILE D 333 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU D 236 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AE2, first strand: chain 'D' and resid 480 through 483 removed outlier: 3.738A pdb=" N GLY D 481 " --> pdb=" O THR D 490 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR D 490 " --> pdb=" O GLY D 481 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'e' and resid 39 through 42 removed outlier: 6.649A pdb=" N ASP h 50 " --> pdb=" O ILE e 551 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN e 553 " --> pdb=" O ASP h 50 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE h 51 " --> pdb=" O SER h 63 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER h 63 " --> pdb=" O ILE h 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'e' and resid 166 through 167 Processing sheet with id=AE5, first strand: chain 'e' and resid 224 through 230 removed outlier: 6.185A pdb=" N LYS e 225 " --> pdb=" O CYS e 406 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL e 408 " --> pdb=" O LYS e 225 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN e 227 " --> pdb=" O VAL e 408 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N GLY e 410 " --> pdb=" O GLN e 227 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG e 229 " --> pdb=" O GLY e 410 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR e 405 " --> pdb=" O ILE e 240 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE e 240 " --> pdb=" O THR e 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'e' and resid 244 through 245 removed outlier: 3.678A pdb=" N LEU e 245 " --> pdb=" O LEU e 393 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE e 380 " --> pdb=" O VAL e 258 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'e' and resid 342 through 344 removed outlier: 6.689A pdb=" N LYS e 268 " --> pdb=" O VAL e 320 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE e 322 " --> pdb=" O LYS e 268 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ALA e 270 " --> pdb=" O ILE e 322 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 39 through 42 removed outlier: 6.547A pdb=" N ASP H 50 " --> pdb=" O ILE E 551 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN E 553 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE H 51 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER H 63 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 166 through 167 Processing sheet with id=AF1, first strand: chain 'E' and resid 224 through 230 removed outlier: 4.021A pdb=" N GLY E 410 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR E 405 " --> pdb=" O ILE E 240 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE E 240 " --> pdb=" O THR E 405 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 342 through 343 removed outlier: 5.885A pdb=" N VAL E 321 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL E 320 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 379 through 383 removed outlier: 4.168A pdb=" N ARG E 379 " --> pdb=" O GLU E 396 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET E 392 " --> pdb=" O GLN E 383 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'g' and resid 55 through 56 removed outlier: 7.699A pdb=" N LEU g 45 " --> pdb=" O GLU z 532 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LEU z 534 " --> pdb=" O LEU g 45 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET g 47 " --> pdb=" O LEU z 534 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ALA z 536 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU g 49 " --> pdb=" O ALA z 536 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'g' and resid 141 through 142 Processing sheet with id=AF6, first strand: chain 'g' and resid 206 through 208 removed outlier: 6.766A pdb=" N GLU g 207 " --> pdb=" O LEU g 381 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'g' and resid 224 through 225 Processing sheet with id=AF8, first strand: chain 'g' and resid 245 through 246 removed outlier: 3.514A pdb=" N LEU g 246 " --> pdb=" O ILE g 296 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 482 through 484 Processing sheet with id=AG1, first strand: chain 'G' and resid 55 through 56 removed outlier: 6.980A pdb=" N LEU G 45 " --> pdb=" O CYS Z 530 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLU Z 532 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET G 47 " --> pdb=" O GLU Z 532 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU Z 534 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AG3, first strand: chain 'G' and resid 206 through 209 Processing sheet with id=AG4, first strand: chain 'G' and resid 224 through 225 Processing sheet with id=AG5, first strand: chain 'G' and resid 243 through 246 removed outlier: 6.494A pdb=" N VAL G 244 " --> pdb=" O ILE G 296 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 482 through 484 Processing sheet with id=AG7, first strand: chain 'h' and resid 17 through 21 removed outlier: 3.953A pdb=" N VAL h 520 " --> pdb=" O ASN q 52 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE q 54 " --> pdb=" O VAL h 520 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU h 522 " --> pdb=" O ILE q 54 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL q 56 " --> pdb=" O GLU h 522 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE h 524 " --> pdb=" O VAL q 56 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'h' and resid 145 through 146 Processing sheet with id=AG9, first strand: chain 'h' and resid 199 through 205 removed outlier: 6.338A pdb=" N GLY h 200 " --> pdb=" O LEU h 376 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU h 378 " --> pdb=" O GLY h 200 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS h 202 " --> pdb=" O LEU h 378 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N GLY h 380 " --> pdb=" O LYS h 202 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE h 204 " --> pdb=" O GLY h 380 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'h' and resid 235 through 236 removed outlier: 3.641A pdb=" N GLU h 353 " --> pdb=" O LEU h 364 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'h' and resid 313 through 315 removed outlier: 6.353A pdb=" N VAL h 293 " --> pdb=" O ALA h 315 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N GLN h 335 " --> pdb=" O ILE h 241 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER h 243 " --> pdb=" O GLN h 335 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'h' and resid 313 through 315 removed outlier: 6.353A pdb=" N VAL h 293 " --> pdb=" O ALA h 315 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'h' and resid 479 through 481 Processing sheet with id=AH5, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.584A pdb=" N SER H 20 " --> pdb=" O THR H 523 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL H 520 " --> pdb=" O ASN Q 52 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE Q 54 " --> pdb=" O VAL H 520 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU H 522 " --> pdb=" O ILE Q 54 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL Q 56 " --> pdb=" O GLU H 522 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE H 524 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 145 through 146 Processing sheet with id=AH7, first strand: chain 'H' and resid 199 through 205 removed outlier: 6.536A pdb=" N GLY H 200 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU H 378 " --> pdb=" O GLY H 200 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS H 202 " --> pdb=" O LEU H 378 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLY H 380 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE H 204 " --> pdb=" O GLY H 380 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 241 through 244 removed outlier: 6.526A pdb=" N VAL H 293 " --> pdb=" O ALA H 315 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 351 through 355 removed outlier: 3.720A pdb=" N GLU H 353 " --> pdb=" O LEU H 364 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 479 through 481 Processing sheet with id=AI2, first strand: chain 'q' and resid 207 through 213 removed outlier: 6.582A pdb=" N ARG q 208 " --> pdb=" O ILE q 384 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU q 386 " --> pdb=" O ARG q 208 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL q 210 " --> pdb=" O LEU q 386 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N GLY q 388 " --> pdb=" O VAL q 210 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE q 212 " --> pdb=" O GLY q 388 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR q 383 " --> pdb=" O ILE q 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE q 223 " --> pdb=" O THR q 383 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE q 385 " --> pdb=" O THR q 221 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR q 221 " --> pdb=" O ILE q 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'q' and resid 319 through 322 removed outlier: 6.596A pdb=" N LYS q 246 " --> pdb=" O VAL q 296 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL q 247 " --> pdb=" O GLY q 353 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'q' and resid 360 through 363 Processing sheet with id=AI5, first strand: chain 'q' and resid 419 through 421 Processing sheet with id=AI6, first strand: chain 'q' and resid 544 through 546 removed outlier: 6.252A pdb=" N ILE q 545 " --> pdb=" O VAL z 47 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS z 44 " --> pdb=" O THR z 56 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR z 56 " --> pdb=" O LYS z 44 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Q' and resid 207 through 213 removed outlier: 3.585A pdb=" N GLY Q 388 " --> pdb=" O ILE Q 212 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Q' and resid 227 through 228 Processing sheet with id=AI9, first strand: chain 'Q' and resid 319 through 322 removed outlier: 6.497A pdb=" N LYS Q 246 " --> pdb=" O CYS Q 298 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL Q 300 " --> pdb=" O LYS Q 246 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ALA Q 248 " --> pdb=" O VAL Q 300 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Q' and resid 419 through 421 Processing sheet with id=AJ2, first strand: chain 'Q' and resid 541 through 545 removed outlier: 4.095A pdb=" N ILE Q 541 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N MET Z 45 " --> pdb=" O ILE Q 541 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N GLN Q 543 " --> pdb=" O MET Z 45 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N VAL Z 47 " --> pdb=" O GLN Q 543 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE Q 545 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS Z 44 " --> pdb=" O THR Z 56 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'z' and resid 138 through 139 Processing sheet with id=AJ4, first strand: chain 'z' and resid 194 through 199 removed outlier: 6.338A pdb=" N GLU z 195 " --> pdb=" O ILE z 378 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE z 380 " --> pdb=" O GLU z 195 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET z 197 " --> pdb=" O ILE z 380 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU z 379 " --> pdb=" O THR z 208 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR z 208 " --> pdb=" O LEU z 379 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'z' and resid 214 through 215 removed outlier: 3.630A pdb=" N THR z 365 " --> pdb=" O LEU z 215 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR z 366 " --> pdb=" O TYR z 355 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR z 355 " --> pdb=" O TYR z 366 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'z' and resid 315 through 316 removed outlier: 3.811A pdb=" N LEU z 315 " --> pdb=" O PHE z 293 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR z 232 " --> pdb=" O VAL z 294 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N GLN z 337 " --> pdb=" O VAL z 233 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE z 235 " --> pdb=" O GLN z 337 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'z' and resid 315 through 316 removed outlier: 3.811A pdb=" N LEU z 315 " --> pdb=" O PHE z 293 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR z 232 " --> pdb=" O VAL z 294 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA z 231 " --> pdb=" O SER z 351 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'z' and resid 490 through 491 Processing sheet with id=AJ9, first strand: chain 'Z' and resid 138 through 139 Processing sheet with id=AK1, first strand: chain 'Z' and resid 194 through 199 removed outlier: 6.026A pdb=" N GLU Z 195 " --> pdb=" O ILE Z 378 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE Z 380 " --> pdb=" O GLU Z 195 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N MET Z 197 " --> pdb=" O ILE Z 380 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU Z 379 " --> pdb=" O THR Z 208 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR Z 208 " --> pdb=" O LEU Z 379 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'Z' and resid 214 through 215 removed outlier: 3.645A pdb=" N LEU Z 215 " --> pdb=" O THR Z 365 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR Z 365 " --> pdb=" O LEU Z 215 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR Z 366 " --> pdb=" O TYR Z 355 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR Z 355 " --> pdb=" O TYR Z 366 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'Z' and resid 315 through 316 removed outlier: 3.571A pdb=" N LEU Z 315 " --> pdb=" O PHE Z 293 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR Z 232 " --> pdb=" O VAL Z 294 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N GLN Z 337 " --> pdb=" O VAL Z 233 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE Z 235 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'Z' and resid 315 through 316 removed outlier: 3.571A pdb=" N LEU Z 315 " --> pdb=" O PHE Z 293 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR Z 232 " --> pdb=" O VAL Z 294 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'Z' and resid 490 through 491 3419 hydrogen bonds defined for protein. 9852 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: 23.94 Time building geometry restraints manager: 19.80 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: 21910 1.34 - 1.46: 11800 1.46 - 1.58: 31036 1.58 - 1.70: 0 1.70 - 1.82: 518 Bond restraints: 65264 Sorted by residual: bond pdb=" C LYS q 413 " pdb=" N PRO q 414 " ideal model delta sigma weight residual 1.334 1.553 -0.219 2.34e-02 1.83e+03 8.75e+01 bond pdb=" C LYS Q 413 " pdb=" N PRO Q 414 " ideal model delta sigma weight residual 1.334 1.552 -0.218 2.34e-02 1.83e+03 8.66e+01 bond pdb=" C GLU q 486 " pdb=" N PRO q 487 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.10e+00 bond pdb=" CA HIS Q 494 " pdb=" CB HIS Q 494 " ideal model delta sigma weight residual 1.530 1.554 -0.024 1.69e-02 3.50e+03 1.98e+00 bond pdb=" C ALA g 108 " pdb=" N PRO g 109 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.23e-02 6.61e+03 1.58e+00 ... (remaining 65259 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.86: 1347 106.86 - 113.65: 37866 113.65 - 120.44: 24060 120.44 - 127.23: 24361 127.23 - 134.02: 404 Bond angle restraints: 88038 Sorted by residual: angle pdb=" N ILE b 245 " pdb=" CA ILE b 245 " pdb=" C ILE b 245 " ideal model delta sigma weight residual 112.83 106.45 6.38 9.90e-01 1.02e+00 4.16e+01 angle pdb=" N ILE G 499 " pdb=" CA ILE G 499 " pdb=" C ILE G 499 " ideal model delta sigma weight residual 112.83 107.18 5.65 9.90e-01 1.02e+00 3.25e+01 angle pdb=" C SER e 171 " pdb=" CA SER e 171 " pdb=" CB SER e 171 " ideal model delta sigma weight residual 117.23 110.44 6.79 1.36e+00 5.41e-01 2.49e+01 angle pdb=" C MET Q 412 " pdb=" N LYS Q 413 " pdb=" CA LYS Q 413 " ideal model delta sigma weight residual 120.97 126.38 -5.41 1.48e+00 4.57e-01 1.34e+01 angle pdb=" C ILE b 467 " pdb=" N SER b 468 " pdb=" CA SER b 468 " ideal model delta sigma weight residual 122.41 117.11 5.30 1.47e+00 4.63e-01 1.30e+01 ... (remaining 88033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 39880 16.00 - 31.99: 372 31.99 - 47.99: 221 47.99 - 63.98: 58 63.98 - 79.98: 3 Dihedral angle restraints: 40534 sinusoidal: 16262 harmonic: 24272 Sorted by residual: dihedral pdb=" CA LYS q 491 " pdb=" C LYS q 491 " pdb=" N THR q 492 " pdb=" CA THR q 492 " ideal model delta harmonic sigma weight residual -180.00 -139.06 -40.94 0 5.00e+00 4.00e-02 6.70e+01 dihedral pdb=" CA SER q 505 " pdb=" C SER q 505 " pdb=" N ASP q 506 " pdb=" CA ASP q 506 " ideal model delta harmonic sigma weight residual -180.00 -141.89 -38.11 0 5.00e+00 4.00e-02 5.81e+01 dihedral pdb=" CA ASP D 183 " pdb=" C ASP D 183 " pdb=" N GLU D 184 " pdb=" CA GLU D 184 " ideal model delta harmonic sigma weight residual -180.00 -152.51 -27.49 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 40531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 7531 0.035 - 0.069: 2023 0.069 - 0.104: 670 0.104 - 0.138: 310 0.138 - 0.173: 8 Chirality restraints: 10542 Sorted by residual: chirality pdb=" CB ILE Z 296 " pdb=" CA ILE Z 296 " pdb=" CG1 ILE Z 296 " pdb=" CG2 ILE Z 296 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CB ILE A 237 " pdb=" CA ILE A 237 " pdb=" CG1 ILE A 237 " pdb=" CG2 ILE A 237 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA ILE A 237 " pdb=" N ILE A 237 " pdb=" C ILE A 237 " pdb=" CB ILE A 237 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 10539 not shown) Planarity restraints: 11350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP d 440 " -0.007 2.00e-02 2.50e+03 1.09e-02 2.96e+00 pdb=" CG TRP d 440 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP d 440 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP d 440 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP d 440 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP d 440 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP d 440 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP d 440 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP d 440 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP d 440 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER g 409 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO g 410 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO g 410 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO g 410 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 225 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ASN A 225 " 0.023 2.00e-02 2.50e+03 pdb=" O ASN A 225 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS A 226 " -0.008 2.00e-02 2.50e+03 ... (remaining 11347 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1026 2.69 - 3.24: 63685 3.24 - 3.79: 92081 3.79 - 4.35: 131691 4.35 - 4.90: 211364 Nonbonded interactions: 499847 Sorted by model distance: nonbonded pdb=" O ASP Q 493 " pdb=" CG HIS Q 494 " model vdw 2.136 3.260 nonbonded pdb=" O GLU Q 504 " pdb=" O SER Q 505 " model vdw 2.159 3.040 nonbonded pdb=" OG SER B 48 " pdb=" OG1 THR B 53 " model vdw 2.184 2.440 nonbonded pdb=" OG SER b 453 " pdb=" O SER B 113 " model vdw 2.194 2.440 nonbonded pdb=" OG SER G 411 " pdb=" OE1 GLU G 503 " model vdw 2.204 2.440 ... (remaining 499842 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' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'z' } Set up NCS constraints Number of NCS constrained groups: 8 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'a' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'b' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'd' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'e' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'g' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'h' } pdb_interpretation.ncs_group { reference = chain 'Q' selection = chain 'q' } pdb_interpretation.ncs_group { reference = chain 'Z' selection = chain 'z' } Set refine NCS operators NCS operators will be refined. 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 6.330 Check model and map are aligned: 0.720 Set scattering table: 0.450 Process input model: 129.000 Find NCS groups from input model: 5.600 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.219 65264 Z= 0.135 Angle : 0.581 10.412 88038 Z= 0.381 Chirality : 0.039 0.173 10542 Planarity : 0.002 0.039 11350 Dihedral : 7.374 79.979 24810 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.38 % Rotamer: Outliers : 0.01 % Allowed : 0.13 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.07), residues: 8414 helix: -3.10 (0.05), residues: 4191 sheet: -1.16 (0.14), residues: 952 loop : -1.69 (0.09), residues: 3271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP d 440 HIS 0.005 0.001 HIS A 209 PHE 0.018 0.001 PHE H 224 TYR 0.012 0.001 TYR b 293 ARG 0.003 0.000 ARG a 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16828 Ramachandran restraints generated. 8414 Oldfield, 0 Emsley, 8414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16828 Ramachandran restraints generated. 8414 Oldfield, 0 Emsley, 8414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1668 time to fit residues: 34.6808 Evaluate side-chains 96 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5062 Evaluate side-chains 165 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1530 time to fit residues: 30.0544 Evaluate side-chains 76 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4805 Evaluate side-chains 164 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1719 time to fit residues: 33.0042 Evaluate side-chains 85 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4960 Evaluate side-chains 165 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.370 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 outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1351 time to fit residues: 27.2151 Evaluate side-chains 105 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5021 Evaluate side-chains 180 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1699 time to fit residues: 35.7656 Evaluate side-chains 87 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4896 Evaluate side-chains 175 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.352 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 outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1813 time to fit residues: 36.8006 Evaluate side-chains 81 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4711 Evaluate side-chains 186 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1494 time to fit residues: 33.4319 Evaluate side-chains 105 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4971 Evaluate side-chains 195 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.365 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1507 time to fit residues: 35.2248 Evaluate side-chains 97 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 705 optimal weight: 0.9980 chunk 633 optimal weight: 5.9990 chunk 351 optimal weight: 4.9990 chunk 216 optimal weight: 20.0000 chunk 427 optimal weight: 0.3980 chunk 338 optimal weight: 0.7980 chunk 655 optimal weight: 9.9990 chunk 253 optimal weight: 7.9990 chunk 398 optimal weight: 3.9990 chunk 487 optimal weight: 20.0000 chunk 759 optimal weight: 0.0670 overall best weight: 1.2520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN B 222 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN D 284 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 GLN E 241 ASN ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 502 GLN E 509 ASN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 188 GLN ** G 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 GLN G 438 GLN G 443 GLN ** G 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 345 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 373 GLN Q 391 GLN Q 472 ASN Q 482 HIS ** Q 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 430 ASN Z 461 ASN ** Z 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.9197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 65264 Z= 0.239 Angle : 0.792 25.813 88038 Z= 0.418 Chirality : 0.047 0.397 10542 Planarity : 0.005 0.071 11350 Dihedral : 4.874 44.556 8928 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.78 % Allowed : 2.97 % Favored : 96.24 % Rotamer: Outliers : 0.34 % Allowed : 3.14 % Favored : 96.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.33 (0.08), residues: 8414 helix: -0.30 (0.07), residues: 4302 sheet: -0.66 (0.15), residues: 1002 loop : -1.65 (0.10), residues: 3110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 500 HIS 0.016 0.001 HIS e 50 PHE 0.037 0.002 PHE b 6 TYR 0.037 0.002 TYR q 131 ARG 0.022 0.001 ARG A 540 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15586 Ramachandran restraints generated. 7793 Oldfield, 0 Emsley, 7793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15586 Ramachandran restraints generated. 7793 Oldfield, 0 Emsley, 7793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 114 average time/residue: 0.1328 time to fit residues: 18.8701 Evaluate side-chains 74 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5040 Evaluate side-chains 95 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1185 time to fit residues: 14.3071 Evaluate side-chains 62 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.483 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4749 Evaluate side-chains 93 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 93 average time/residue: 0.1317 time to fit residues: 15.2368 Evaluate side-chains 58 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0519 time to fit residues: 0.5637 Evaluate side-chains 105 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.1194 time to fit residues: 15.8525 Evaluate side-chains 74 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5112 Evaluate side-chains 116 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.354 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 outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1455 time to fit residues: 20.2480 Evaluate side-chains 69 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4910 Evaluate side-chains 112 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 110 average time/residue: 0.1282 time to fit residues: 17.5006 Evaluate side-chains 71 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4746 Evaluate side-chains 127 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.1200 time to fit residues: 19.2764 Evaluate side-chains 90 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4964 Evaluate side-chains 125 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.1298 time to fit residues: 20.1763 Evaluate side-chains 86 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 421 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 631 optimal weight: 7.9990 chunk 516 optimal weight: 6.9990 chunk 209 optimal weight: 20.0000 chunk 760 optimal weight: 5.9990 chunk 821 optimal weight: 0.0570 chunk 677 optimal weight: 6.9990 chunk 754 optimal weight: 0.4980 chunk 259 optimal weight: 7.9990 chunk 610 optimal weight: 50.0000 overall best weight: 3.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN ** G 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 394 HIS ** H 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 154 ASN Q 373 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 297 ASN ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 390 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.9738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.416 65264 Z= 0.464 Angle : 1.205 67.085 88038 Z= 0.613 Chirality : 0.095 5.041 10542 Planarity : 0.010 0.200 11350 Dihedral : 5.236 38.521 8928 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.85 % Favored : 95.63 % Rotamer: Outliers : 0.84 % Allowed : 3.65 % Favored : 95.51 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.42 (0.08), residues: 8414 helix: -0.37 (0.07), residues: 4306 sheet: -0.59 (0.15), residues: 998 loop : -1.73 (0.10), residues: 3110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 345 HIS 0.034 0.003 HIS a 514 PHE 0.100 0.005 PHE A 175 TYR 0.175 0.006 TYR A 497 ARG 0.083 0.003 ARG a 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15586 Ramachandran restraints generated. 7793 Oldfield, 0 Emsley, 7793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15586 Ramachandran restraints generated. 7793 Oldfield, 0 Emsley, 7793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 8 residues processed: 121 average time/residue: 0.1417 time to fit residues: 21.0482 Evaluate side-chains 75 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0646 time to fit residues: 1.2441 Evaluate side-chains 84 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1050 time to fit residues: 11.5144 Evaluate side-chains 59 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4741 Evaluate side-chains 76 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1089 time to fit residues: 10.8101 Evaluate side-chains 52 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4938 Evaluate side-chains 84 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1056 time to fit residues: 11.6551 Evaluate side-chains 68 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5030 Evaluate side-chains 96 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1327 time to fit residues: 15.5883 Evaluate side-chains 66 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4847 Evaluate side-chains 96 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1269 time to fit residues: 15.1929 Evaluate side-chains 67 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4714 Evaluate side-chains 111 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1259 time to fit residues: 17.5801 Evaluate side-chains 83 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4904 Evaluate side-chains 101 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0961 time to fit residues: 13.0318 Evaluate side-chains 75 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.1774 > 50: distance: 0 - 1: 5.961 distance: 1 - 2: 7.723 distance: 1 - 7: 16.200 distance: 3 - 4: 3.006 distance: 7 - 8: 21.957 distance: 8 - 9: 16.709 distance: 8 - 11: 16.777 distance: 9 - 10: 24.079 distance: 9 - 15: 12.389 distance: 11 - 12: 12.866 distance: 12 - 13: 11.492 distance: 12 - 14: 12.279 distance: 15 - 16: 14.964 distance: 16 - 17: 7.144 distance: 16 - 19: 13.401 distance: 17 - 18: 15.042 distance: 17 - 20: 10.267 distance: 20 - 21: 25.760 distance: 21 - 22: 13.752 distance: 22 - 23: 13.257 distance: 22 - 24: 16.550 distance: 24 - 25: 45.209 distance: 25 - 26: 63.177 distance: 25 - 28: 36.379 distance: 26 - 27: 47.834 distance: 26 - 29: 22.112 distance: 29 - 30: 22.680 distance: 30 - 31: 10.980 distance: 30 - 33: 31.182 distance: 31 - 32: 13.916 distance: 31 - 38: 7.701 distance: 33 - 34: 48.239 distance: 34 - 35: 32.552 distance: 35 - 36: 8.346 distance: 35 - 37: 6.338 distance: 38 - 39: 11.595 distance: 39 - 40: 6.900 distance: 39 - 42: 23.114 distance: 40 - 41: 10.666 distance: 40 - 45: 16.806 distance: 42 - 43: 50.254 distance: 42 - 44: 27.519 distance: 45 - 46: 6.283 distance: 46 - 47: 16.049 distance: 46 - 49: 13.510 distance: 47 - 48: 21.888 distance: 47 - 52: 12.889 distance: 49 - 50: 17.096 distance: 49 - 51: 12.663 distance: 52 - 53: 25.460 distance: 53 - 54: 11.029 distance: 53 - 56: 24.117 distance: 54 - 55: 12.955 distance: 54 - 60: 16.501 distance: 56 - 57: 21.646 distance: 57 - 58: 32.544 distance: 57 - 59: 27.092 distance: 60 - 61: 8.900 distance: 61 - 62: 5.580 distance: 61 - 64: 3.208 distance: 62 - 63: 6.178 distance: 62 - 67: 6.457 distance: 64 - 65: 3.447 distance: 64 - 66: 6.601