Starting phenix.real_space_refine on Fri Dec 15 08:45:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnk_29316/12_2023/8fnk_29316.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnk_29316/12_2023/8fnk_29316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnk_29316/12_2023/8fnk_29316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnk_29316/12_2023/8fnk_29316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnk_29316/12_2023/8fnk_29316.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnk_29316/12_2023/8fnk_29316.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 94 5.49 5 S 188 5.16 5 C 19153 2.51 5 N 5409 2.21 5 O 5987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "6 PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 432": "OE1" <-> "OE2" Residue "6 TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 70": "OD1" <-> "OD2" Residue "8 GLU 115": "OE1" <-> "OE2" Residue "8 GLU 137": "OE1" <-> "OE2" Residue "8 TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 366": "OE1" <-> "OE2" Residue "8 PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 446": "OD1" <-> "OD2" Residue "9 PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 155": "OE1" <-> "OE2" Residue "9 ASP 180": "OD1" <-> "OD2" Residue "9 PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 643": "OD1" <-> "OD2" Residue "9 ASP 644": "OD1" <-> "OD2" Residue "9 GLU 712": "OE1" <-> "OE2" Residue "9 ASP 758": "OD1" <-> "OD2" Residue "9 TYR 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "10 TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "11 PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "11 PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "11 ASP 742": "OD1" <-> "OD2" Residue "11 GLU 757": "OE1" <-> "OE2" Residue "14 GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30831 Number of models: 1 Model: "" Number of chains: 11 Chain: "m" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1053 Classifications: {'RNA': 51} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 34} Link IDs: {'rna2p': 15, 'rna3p': 35} Chain: "g" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 914 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 8, 'rna3p_pur': 25, 'rna3p_pyr': 8} Link IDs: {'rna2p': 10, 'rna3p': 32} Chain: "5" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2318 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 15, 'TRANS': 280} Chain: "6" Number of atoms: 3591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3591 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 11, 'TRANS': 441} Chain: "7" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain breaks: 1 Chain: "8" Number of atoms: 4056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4056 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 24, 'TRANS': 488} Chain: "9" Number of atoms: 6662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6662 Classifications: {'peptide': 858} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 34, 'TRANS': 823} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "10" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3290 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 14, 'TRANS': 401} Chain breaks: 3 Chain: "11" Number of atoms: 4919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4919 Classifications: {'peptide': 614} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 579} Chain breaks: 3 Chain: "13" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1005 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain breaks: 1 Chain: "14" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2505 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 24, 'TRANS': 290} Time building chain proxies: 17.80, per 1000 atoms: 0.58 Number of scatterers: 30831 At special positions: 0 Unit cell: (122.1, 148.5, 286, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 188 16.00 P 94 15.00 O 5987 8.00 N 5409 7.00 C 19153 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: 13.73 Conformation dependent library (CDL) restraints added in 5.9 seconds 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6966 Finding SS restraints... Secondary structure from input PDB file: 214 helices and 10 sheets defined 71.5% alpha, 2.8% beta 24 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 9.79 Creating SS restraints... Processing helix chain '5' and resid 19 through 23 removed outlier: 3.655A pdb=" N ILE 5 23 " --> pdb=" O TYR 5 20 " (cutoff:3.500A) Processing helix chain '5' and resid 34 through 51 removed outlier: 3.855A pdb=" N VAL 5 39 " --> pdb=" O ARG 5 35 " (cutoff:3.500A) Processing helix chain '5' and resid 66 through 71 Processing helix chain '5' and resid 91 through 93 No H-bonds generated for 'chain '5' and resid 91 through 93' Processing helix chain '5' and resid 94 through 109 removed outlier: 3.564A pdb=" N PHE 5 98 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) Processing helix chain '5' and resid 116 through 121 removed outlier: 4.012A pdb=" N ASP 5 120 " --> pdb=" O SER 5 116 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR 5 121 " --> pdb=" O TYR 5 117 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 116 through 121' Processing helix chain '5' and resid 147 through 159 Processing helix chain '5' and resid 180 through 183 Processing helix chain '5' and resid 198 through 212 Processing helix chain '5' and resid 247 through 257 removed outlier: 3.797A pdb=" N ASP 5 251 " --> pdb=" O GLU 5 247 " (cutoff:3.500A) Processing helix chain '5' and resid 265 through 271 removed outlier: 3.861A pdb=" N LYS 5 270 " --> pdb=" O SER 5 266 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU 5 271 " --> pdb=" O GLU 5 267 " (cutoff:3.500A) Processing helix chain '5' and resid 275 through 279 removed outlier: 3.544A pdb=" N VAL 5 279 " --> pdb=" O ARG 5 276 " (cutoff:3.500A) Processing helix chain '6' and resid 62 through 80 Processing helix chain '6' and resid 83 through 96 removed outlier: 3.513A pdb=" N ALA 6 87 " --> pdb=" O ASN 6 83 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA 6 96 " --> pdb=" O ARG 6 92 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 119 removed outlier: 3.581A pdb=" N VAL 6 109 " --> pdb=" O ASP 6 105 " (cutoff:3.500A) Processing helix chain '6' and resid 125 through 138 removed outlier: 3.643A pdb=" N TYR 6 134 " --> pdb=" O GLU 6 130 " (cutoff:3.500A) Processing helix chain '6' and resid 139 through 142 Processing helix chain '6' and resid 146 through 154 Processing helix chain '6' and resid 159 through 174 removed outlier: 3.508A pdb=" N ALA 6 174 " --> pdb=" O ALA 6 170 " (cutoff:3.500A) Processing helix chain '6' and resid 181 through 196 removed outlier: 3.711A pdb=" N THR 6 195 " --> pdb=" O ALA 6 191 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY 6 196 " --> pdb=" O PHE 6 192 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 215 removed outlier: 3.789A pdb=" N ARG 6 215 " --> pdb=" O GLN 6 211 " (cutoff:3.500A) Processing helix chain '6' and resid 220 through 234 removed outlier: 3.513A pdb=" N LEU 6 234 " --> pdb=" O ALA 6 230 " (cutoff:3.500A) Processing helix chain '6' and resid 238 through 251 removed outlier: 3.552A pdb=" N PHE 6 242 " --> pdb=" O ASP 6 238 " (cutoff:3.500A) Processing helix chain '6' and resid 257 through 272 Proline residue: 6 263 - end of helix removed outlier: 4.338A pdb=" N GLY 6 272 " --> pdb=" O PHE 6 268 " (cutoff:3.500A) Processing helix chain '6' and resid 275 through 288 removed outlier: 3.761A pdb=" N SER 6 279 " --> pdb=" O ASP 6 275 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU 6 288 " --> pdb=" O THR 6 284 " (cutoff:3.500A) Processing helix chain '6' and resid 294 through 309 Processing helix chain '6' and resid 312 through 326 removed outlier: 4.020A pdb=" N GLU 6 325 " --> pdb=" O ASN 6 321 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU 6 326 " --> pdb=" O ARG 6 322 " (cutoff:3.500A) Processing helix chain '6' and resid 331 through 346 Processing helix chain '6' and resid 349 through 363 Processing helix chain '6' and resid 364 through 367 Processing helix chain '6' and resid 368 through 383 removed outlier: 3.800A pdb=" N THR 6 377 " --> pdb=" O SER 6 373 " (cutoff:3.500A) Processing helix chain '6' and resid 386 through 400 removed outlier: 3.761A pdb=" N SER 6 399 " --> pdb=" O SER 6 395 " (cutoff:3.500A) Processing helix chain '6' and resid 401 through 404 removed outlier: 3.947A pdb=" N PHE 6 404 " --> pdb=" O ALA 6 401 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 401 through 404' Processing helix chain '6' and resid 405 through 420 removed outlier: 3.863A pdb=" N VAL 6 410 " --> pdb=" O ALA 6 406 " (cutoff:3.500A) Processing helix chain '6' and resid 423 through 438 removed outlier: 3.760A pdb=" N ARG 6 433 " --> pdb=" O ALA 6 429 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER 6 434 " --> pdb=" O LEU 6 430 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL 6 435 " --> pdb=" O SER 6 431 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TYR 6 436 " --> pdb=" O GLU 6 432 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL 6 437 " --> pdb=" O ARG 6 433 " (cutoff:3.500A) Processing helix chain '6' and resid 442 through 457 Processing helix chain '6' and resid 460 through 474 Proline residue: 6 466 - end of helix Processing helix chain '6' and resid 474 through 479 Processing helix chain '6' and resid 486 through 496 removed outlier: 4.103A pdb=" N GLU 6 490 " --> pdb=" O GLU 6 486 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE 6 491 " --> pdb=" O GLU 6 487 " (cutoff:3.500A) Processing helix chain '6' and resid 500 through 509 Processing helix chain '7' and resid 81 through 97 Processing helix chain '7' and resid 106 through 110 Processing helix chain '7' and resid 111 through 116 removed outlier: 3.805A pdb=" N LEU 7 115 " --> pdb=" O ALA 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 119 through 124 removed outlier: 3.528A pdb=" N ILE 7 123 " --> pdb=" O THR 7 119 " (cutoff:3.500A) Processing helix chain '7' and resid 127 through 143 Processing helix chain '8' and resid 22 through 33 Processing helix chain '8' and resid 39 through 53 removed outlier: 3.513A pdb=" N MET 8 53 " --> pdb=" O THR 8 49 " (cutoff:3.500A) Processing helix chain '8' and resid 61 through 75 Processing helix chain '8' and resid 81 through 95 removed outlier: 4.200A pdb=" N VAL 8 95 " --> pdb=" O THR 8 91 " (cutoff:3.500A) Processing helix chain '8' and resid 113 through 127 removed outlier: 3.677A pdb=" N LEU 8 117 " --> pdb=" O SER 8 113 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE 8 118 " --> pdb=" O PRO 8 114 " (cutoff:3.500A) Processing helix chain '8' and resid 131 through 143 removed outlier: 3.727A pdb=" N ILE 8 135 " --> pdb=" O ASP 8 131 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE 8 143 " --> pdb=" O LEU 8 139 " (cutoff:3.500A) Processing helix chain '8' and resid 145 through 149 removed outlier: 3.728A pdb=" N PHE 8 149 " --> pdb=" O LEU 8 146 " (cutoff:3.500A) Processing helix chain '8' and resid 150 through 162 removed outlier: 3.551A pdb=" N LEU 8 154 " --> pdb=" O SER 8 150 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER 8 155 " --> pdb=" O PRO 8 151 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU 8 156 " --> pdb=" O THR 8 152 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR 8 159 " --> pdb=" O SER 8 155 " (cutoff:3.500A) Processing helix chain '8' and resid 168 through 182 removed outlier: 3.828A pdb=" N VAL 8 172 " --> pdb=" O ASN 8 168 " (cutoff:3.500A) Processing helix chain '8' and resid 183 through 186 removed outlier: 3.726A pdb=" N LEU 8 186 " --> pdb=" O ASN 8 183 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 183 through 186' Processing helix chain '8' and resid 187 through 199 Processing helix chain '8' and resid 205 through 219 removed outlier: 3.614A pdb=" N LEU 8 209 " --> pdb=" O SER 8 205 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG 8 219 " --> pdb=" O ILE 8 215 " (cutoff:3.500A) Processing helix chain '8' and resid 220 through 223 Processing helix chain '8' and resid 224 through 239 removed outlier: 3.950A pdb=" N ILE 8 229 " --> pdb=" O PRO 8 225 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN 8 230 " --> pdb=" O GLU 8 226 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL 8 231 " --> pdb=" O ASP 8 227 " (cutoff:3.500A) Processing helix chain '8' and resid 242 through 254 removed outlier: 3.505A pdb=" N PHE 8 246 " --> pdb=" O PHE 8 242 " (cutoff:3.500A) Processing helix chain '8' and resid 261 through 276 Processing helix chain '8' and resid 279 through 294 removed outlier: 4.006A pdb=" N ILE 8 283 " --> pdb=" O GLN 8 279 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE 8 285 " --> pdb=" O GLU 8 281 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU 8 292 " --> pdb=" O ASP 8 288 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL 8 293 " --> pdb=" O ALA 8 289 " (cutoff:3.500A) Processing helix chain '8' and resid 295 through 297 No H-bonds generated for 'chain '8' and resid 295 through 297' Processing helix chain '8' and resid 298 through 312 Processing helix chain '8' and resid 316 through 332 removed outlier: 3.679A pdb=" N THR 8 322 " --> pdb=" O THR 8 318 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG 8 329 " --> pdb=" O SER 8 325 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR 8 330 " --> pdb=" O CYS 8 326 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA 8 332 " --> pdb=" O ILE 8 328 " (cutoff:3.500A) Processing helix chain '8' and resid 333 through 334 No H-bonds generated for 'chain '8' and resid 333 through 334' Processing helix chain '8' and resid 335 through 338 Processing helix chain '8' and resid 339 through 348 removed outlier: 3.507A pdb=" N THR 8 348 " --> pdb=" O ASP 8 344 " (cutoff:3.500A) Processing helix chain '8' and resid 353 through 367 removed outlier: 3.653A pdb=" N GLU 8 366 " --> pdb=" O ASP 8 362 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS 8 367 " --> pdb=" O ARG 8 363 " (cutoff:3.500A) Processing helix chain '8' and resid 372 through 383 removed outlier: 3.537A pdb=" N LEU 8 376 " --> pdb=" O THR 8 372 " (cutoff:3.500A) Processing helix chain '8' and resid 386 through 391 removed outlier: 3.800A pdb=" N GLU 8 391 " --> pdb=" O PRO 8 388 " (cutoff:3.500A) Processing helix chain '8' and resid 392 through 395 Processing helix chain '8' and resid 396 through 406 Processing helix chain '8' and resid 410 through 424 Processing helix chain '8' and resid 428 through 441 removed outlier: 4.327A pdb=" N TYR 8 432 " --> pdb=" O ASP 8 428 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA 8 433 " --> pdb=" O PRO 8 429 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG 8 441 " --> pdb=" O GLU 8 437 " (cutoff:3.500A) Processing helix chain '8' and resid 446 through 458 removed outlier: 3.538A pdb=" N LEU 8 450 " --> pdb=" O ASP 8 446 " (cutoff:3.500A) Proline residue: 8 452 - end of helix Processing helix chain '8' and resid 464 through 479 removed outlier: 3.530A pdb=" N VAL 8 468 " --> pdb=" O PRO 8 464 " (cutoff:3.500A) Proline residue: 8 477 - end of helix Processing helix chain '8' and resid 483 through 497 removed outlier: 3.602A pdb=" N GLU 8 488 " --> pdb=" O LEU 8 484 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG 8 489 " --> pdb=" O MET 8 485 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG 8 496 " --> pdb=" O ARG 8 492 " (cutoff:3.500A) Processing helix chain '8' and resid 504 through 516 removed outlier: 3.609A pdb=" N PHE 8 515 " --> pdb=" O ARG 8 511 " (cutoff:3.500A) Processing helix chain '8' and resid 524 through 532 Processing helix chain '9' and resid 2 through 8 removed outlier: 4.382A pdb=" N LEU 9 6 " --> pdb=" O LEU 9 2 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU 9 7 " --> pdb=" O LEU 9 3 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG 9 8 " --> pdb=" O PRO 9 4 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 2 through 8' Processing helix chain '9' and resid 10 through 15 removed outlier: 4.161A pdb=" N ARG 9 15 " --> pdb=" O GLU 9 11 " (cutoff:3.500A) Processing helix chain '9' and resid 20 through 37 removed outlier: 3.956A pdb=" N ALA 9 36 " --> pdb=" O LEU 9 32 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR 9 37 " --> pdb=" O ASP 9 33 " (cutoff:3.500A) Processing helix chain '9' and resid 41 through 57 removed outlier: 4.003A pdb=" N VAL 9 45 " --> pdb=" O ALA 9 41 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA 9 47 " --> pdb=" O THR 9 43 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS 9 48 " --> pdb=" O LYS 9 44 " (cutoff:3.500A) Proline residue: 9 49 - end of helix removed outlier: 4.122A pdb=" N ARG 9 52 " --> pdb=" O LYS 9 48 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP 9 57 " --> pdb=" O PHE 9 53 " (cutoff:3.500A) Processing helix chain '9' and resid 57 through 66 removed outlier: 3.659A pdb=" N VAL 9 64 " --> pdb=" O THR 9 60 " (cutoff:3.500A) Processing helix chain '9' and resid 74 through 88 Processing helix chain '9' and resid 94 through 110 Processing helix chain '9' and resid 115 through 130 removed outlier: 3.895A pdb=" N TYR 9 119 " --> pdb=" O ASP 9 115 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG 9 120 " --> pdb=" O LEU 9 116 " (cutoff:3.500A) Processing helix chain '9' and resid 134 through 151 removed outlier: 4.168A pdb=" N GLU 9 142 " --> pdb=" O ALA 9 138 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER 9 145 " --> pdb=" O GLU 9 141 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR 9 150 " --> pdb=" O SER 9 146 " (cutoff:3.500A) Processing helix chain '9' and resid 155 through 166 removed outlier: 3.588A pdb=" N LEU 9 166 " --> pdb=" O ILE 9 162 " (cutoff:3.500A) Processing helix chain '9' and resid 167 through 170 removed outlier: 3.618A pdb=" N LYS 9 170 " --> pdb=" O PRO 9 167 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 167 through 170' Processing helix chain '9' and resid 172 through 185 removed outlier: 4.222A pdb=" N GLN 9 176 " --> pdb=" O SER 9 172 " (cutoff:3.500A) Processing helix chain '9' and resid 190 through 202 Processing helix chain '9' and resid 208 through 218 removed outlier: 4.455A pdb=" N GLU 9 218 " --> pdb=" O ALA 9 214 " (cutoff:3.500A) Processing helix chain '9' and resid 219 through 224 removed outlier: 3.575A pdb=" N PHE 9 222 " --> pdb=" O ALA 9 219 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA 9 223 " --> pdb=" O ILE 9 220 " (cutoff:3.500A) Processing helix chain '9' and resid 227 through 241 Processing helix chain '9' and resid 242 through 246 removed outlier: 3.579A pdb=" N ALA 9 245 " --> pdb=" O GLU 9 242 " (cutoff:3.500A) Processing helix chain '9' and resid 247 through 259 removed outlier: 4.021A pdb=" N VAL 9 251 " --> pdb=" O SER 9 247 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS 9 253 " --> pdb=" O ASP 9 249 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU 9 254 " --> pdb=" O ALA 9 250 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU 9 256 " --> pdb=" O LYS 9 252 " (cutoff:3.500A) Processing helix chain '9' and resid 265 through 278 Processing helix chain '9' and resid 287 through 307 removed outlier: 4.192A pdb=" N GLU 9 307 " --> pdb=" O LYS 9 303 " (cutoff:3.500A) Processing helix chain '9' and resid 309 through 313 Processing helix chain '9' and resid 321 through 326 Processing helix chain '9' and resid 327 through 334 Processing helix chain '9' and resid 345 through 361 Processing helix chain '9' and resid 362 through 368 removed outlier: 3.640A pdb=" N ILE 9 366 " --> pdb=" O ARG 9 362 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL 9 367 " --> pdb=" O LEU 9 363 " (cutoff:3.500A) Processing helix chain '9' and resid 372 through 375 removed outlier: 4.596A pdb=" N SER 9 375 " --> pdb=" O PRO 9 372 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 372 through 375' Processing helix chain '9' and resid 376 through 383 removed outlier: 3.595A pdb=" N LEU 9 380 " --> pdb=" O ILE 9 376 " (cutoff:3.500A) Processing helix chain '9' and resid 385 through 403 removed outlier: 3.901A pdb=" N ARG 9 389 " --> pdb=" O MET 9 385 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS 9 391 " --> pdb=" O GLU 9 387 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE 9 396 " --> pdb=" O GLY 9 392 " (cutoff:3.500A) Processing helix chain '9' and resid 407 through 422 Processing helix chain '9' and resid 426 through 438 removed outlier: 3.752A pdb=" N HIS 9 431 " --> pdb=" O ARG 9 427 " (cutoff:3.500A) Processing helix chain '9' and resid 444 through 457 removed outlier: 3.716A pdb=" N ARG 9 457 " --> pdb=" O LYS 9 453 " (cutoff:3.500A) Processing helix chain '9' and resid 469 through 499 removed outlier: 3.921A pdb=" N GLU 9 473 " --> pdb=" O ASP 9 469 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE 9 487 " --> pdb=" O ALA 9 483 " (cutoff:3.500A) Processing helix chain '9' and resid 501 through 515 Processing helix chain '9' and resid 522 through 533 Processing helix chain '9' and resid 543 through 554 Processing helix chain '9' and resid 555 through 562 Processing helix chain '9' and resid 562 through 575 Processing helix chain '9' and resid 579 through 583 removed outlier: 3.665A pdb=" N LEU 9 583 " --> pdb=" O GLU 9 580 " (cutoff:3.500A) Processing helix chain '9' and resid 584 through 593 Processing helix chain '9' and resid 602 through 617 removed outlier: 3.878A pdb=" N GLU 9 607 " --> pdb=" O GLU 9 603 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY 9 608 " --> pdb=" O ILE 9 604 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP 9 609 " --> pdb=" O GLN 9 605 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU 9 617 " --> pdb=" O ASN 9 613 " (cutoff:3.500A) Processing helix chain '9' and resid 622 through 634 Processing helix chain '9' and resid 635 through 637 No H-bonds generated for 'chain '9' and resid 635 through 637' Processing helix chain '9' and resid 644 through 656 removed outlier: 3.728A pdb=" N PHE 9 652 " --> pdb=" O PHE 9 648 " (cutoff:3.500A) Processing helix chain '9' and resid 659 through 673 removed outlier: 3.518A pdb=" N LEU 9 663 " --> pdb=" O GLN 9 659 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLN 9 665 " --> pdb=" O ARG 9 661 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS 9 666 " --> pdb=" O ILE 9 662 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL 9 671 " --> pdb=" O LEU 9 667 " (cutoff:3.500A) Processing helix chain '9' and resid 680 through 692 removed outlier: 3.709A pdb=" N ASN 9 689 " --> pdb=" O GLY 9 685 " (cutoff:3.500A) Processing helix chain '9' and resid 698 through 709 removed outlier: 3.763A pdb=" N VAL 9 702 " --> pdb=" O TYR 9 698 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE 9 709 " --> pdb=" O PHE 9 705 " (cutoff:3.500A) Processing helix chain '9' and resid 710 through 715 removed outlier: 3.964A pdb=" N TRP 9 714 " --> pdb=" O SER 9 710 " (cutoff:3.500A) Processing helix chain '9' and resid 718 through 732 removed outlier: 3.508A pdb=" N LYS 9 724 " --> pdb=" O SER 9 720 " (cutoff:3.500A) Processing helix chain '9' and resid 736 through 751 removed outlier: 3.679A pdb=" N LEU 9 740 " --> pdb=" O LEU 9 736 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL 9 741 " --> pdb=" O PRO 9 737 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS 9 742 " --> pdb=" O GLN 9 738 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU 9 748 " --> pdb=" O GLY 9 744 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP 9 749 " --> pdb=" O ASP 9 745 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL 9 750 " --> pdb=" O ARG 9 746 " (cutoff:3.500A) Processing helix chain '9' and resid 752 through 754 No H-bonds generated for 'chain '9' and resid 752 through 754' Processing helix chain '9' and resid 755 through 768 removed outlier: 3.585A pdb=" N ASN 9 764 " --> pdb=" O ALA 9 760 " (cutoff:3.500A) Processing helix chain '9' and resid 773 through 787 removed outlier: 3.629A pdb=" N LEU 9 777 " --> pdb=" O ASN 9 773 " (cutoff:3.500A) Processing helix chain '9' and resid 788 through 791 Processing helix chain '9' and resid 792 through 801 Processing helix chain '9' and resid 804 through 809 removed outlier: 3.683A pdb=" N ARG 9 807 " --> pdb=" O GLY 9 804 " (cutoff:3.500A) Processing helix chain '9' and resid 815 through 826 removed outlier: 3.868A pdb=" N GLU 9 820 " --> pdb=" O ALA 9 816 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLN 9 821 " --> pdb=" O PRO 9 817 " (cutoff:3.500A) Processing helix chain '9' and resid 828 through 840 removed outlier: 4.039A pdb=" N ARG 9 840 " --> pdb=" O ALA 9 836 " (cutoff:3.500A) Processing helix chain '9' and resid 845 through 857 removed outlier: 3.660A pdb=" N LEU 9 855 " --> pdb=" O SER 9 851 " (cutoff:3.500A) Processing helix chain '10' and resid 117 through 141 removed outlier: 4.057A pdb=" N ALA10 121 " --> pdb=" O THR10 117 " (cutoff:3.500A) Processing helix chain '10' and resid 155 through 183 removed outlier: 4.001A pdb=" N GLU10 160 " --> pdb=" O GLU10 156 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE10 161 " --> pdb=" O GLY10 157 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR10 183 " --> pdb=" O GLN10 179 " (cutoff:3.500A) Processing helix chain '10' and resid 190 through 207 removed outlier: 3.543A pdb=" N LEU10 194 " --> pdb=" O GLY10 190 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS10 205 " --> pdb=" O THR10 201 " (cutoff:3.500A) Processing helix chain '10' and resid 211 through 233 Processing helix chain '10' and resid 236 through 249 removed outlier: 3.724A pdb=" N THR10 249 " --> pdb=" O THR10 245 " (cutoff:3.500A) Processing helix chain '10' and resid 254 through 265 Processing helix chain '10' and resid 266 through 272 removed outlier: 6.097A pdb=" N SER10 269 " --> pdb=" O LEU10 266 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU10 272 " --> pdb=" O SER10 269 " (cutoff:3.500A) Processing helix chain '10' and resid 275 through 289 removed outlier: 3.539A pdb=" N LYS10 280 " --> pdb=" O MET10 276 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR10 289 " --> pdb=" O ARG10 285 " (cutoff:3.500A) Processing helix chain '10' and resid 290 through 293 Processing helix chain '10' and resid 294 through 296 No H-bonds generated for 'chain '10' and resid 294 through 296' Processing helix chain '10' and resid 297 through 308 removed outlier: 3.978A pdb=" N MET10 308 " --> pdb=" O VAL10 304 " (cutoff:3.500A) Processing helix chain '10' and resid 308 through 316 removed outlier: 3.873A pdb=" N VAL10 312 " --> pdb=" O MET10 308 " (cutoff:3.500A) Processing helix chain '10' and resid 320 through 334 removed outlier: 3.901A pdb=" N LEU10 325 " --> pdb=" O LEU10 321 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS10 334 " --> pdb=" O CYS10 330 " (cutoff:3.500A) Processing helix chain '10' and resid 338 through 340 No H-bonds generated for 'chain '10' and resid 338 through 340' Processing helix chain '10' and resid 341 through 351 removed outlier: 4.056A pdb=" N ALA10 345 " --> pdb=" O LEU10 341 " (cutoff:3.500A) Processing helix chain '10' and resid 352 through 355 removed outlier: 3.726A pdb=" N PHE10 355 " --> pdb=" O VAL10 352 " (cutoff:3.500A) No H-bonds generated for 'chain '10' and resid 352 through 355' Processing helix chain '10' and resid 356 through 370 removed outlier: 3.506A pdb=" N HIS10 365 " --> pdb=" O ALA10 361 " (cutoff:3.500A) Processing helix chain '10' and resid 374 through 387 removed outlier: 3.515A pdb=" N CYS10 378 " --> pdb=" O ARG10 374 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU10 383 " --> pdb=" O GLU10 379 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG10 384 " --> pdb=" O ARG10 380 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE10 385 " --> pdb=" O LEU10 381 " (cutoff:3.500A) Processing helix chain '10' and resid 392 through 410 removed outlier: 3.571A pdb=" N VAL10 410 " --> pdb=" O CYS10 406 " (cutoff:3.500A) Processing helix chain '10' and resid 419 through 436 removed outlier: 3.749A pdb=" N LYS10 426 " --> pdb=" O PRO10 422 " (cutoff:3.500A) Processing helix chain '10' and resid 437 through 441 removed outlier: 3.609A pdb=" N GLU10 440 " --> pdb=" O ARG10 437 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL10 441 " --> pdb=" O LEU10 438 " (cutoff:3.500A) No H-bonds generated for 'chain '10' and resid 437 through 441' Processing helix chain '10' and resid 445 through 460 removed outlier: 3.638A pdb=" N ILE10 449 " --> pdb=" O ALA10 445 " (cutoff:3.500A) Processing helix chain '10' and resid 464 through 485 removed outlier: 4.125A pdb=" N ILE10 481 " --> pdb=" O ASP10 477 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL10 482 " --> pdb=" O MET10 478 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET10 483 " --> pdb=" O VAL10 479 " (cutoff:3.500A) Processing helix chain '10' and resid 502 through 517 Processing helix chain '10' and resid 518 through 521 Processing helix chain '10' and resid 523 through 535 Processing helix chain '11' and resid 194 through 205 Processing helix chain '11' and resid 214 through 228 Proline residue: 11 223 - end of helix Processing helix chain '11' and resid 233 through 243 Processing helix chain '11' and resid 246 through 253 Processing helix chain '11' and resid 253 through 276 removed outlier: 4.120A pdb=" N ASP11 259 " --> pdb=" O THR11 255 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG11 264 " --> pdb=" O MET11 260 " (cutoff:3.500A) Processing helix chain '11' and resid 322 through 326 removed outlier: 3.631A pdb=" N ARG11 326 " --> pdb=" O LEU11 322 " (cutoff:3.500A) No H-bonds generated for 'chain '11' and resid 322 through 326' Processing helix chain '11' and resid 332 through 342 Processing helix chain '11' and resid 350 through 367 removed outlier: 3.791A pdb=" N MET11 360 " --> pdb=" O PHE11 356 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N MET11 362 " --> pdb=" O GLN11 358 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE11 363 " --> pdb=" O ALA11 359 " (cutoff:3.500A) Processing helix chain '11' and resid 368 through 371 Processing helix chain '11' and resid 373 through 387 removed outlier: 4.114A pdb=" N LEU11 377 " --> pdb=" O ASP11 373 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL11 378 " --> pdb=" O PRO11 374 " (cutoff:3.500A) Processing helix chain '11' and resid 392 through 408 removed outlier: 3.879A pdb=" N ALA11 404 " --> pdb=" O GLY11 400 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL11 405 " --> pdb=" O ARG11 401 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS11 408 " --> pdb=" O ALA11 404 " (cutoff:3.500A) Processing helix chain '11' and resid 413 through 427 Processing helix chain '11' and resid 432 through 463 Processing helix chain '11' and resid 524 through 541 removed outlier: 4.323A pdb=" N ARG11 531 " --> pdb=" O LEU11 527 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA11 532 " --> pdb=" O GLN11 528 " (cutoff:3.500A) Processing helix chain '11' and resid 543 through 558 removed outlier: 4.264A pdb=" N LYS11 549 " --> pdb=" O SER11 545 " (cutoff:3.500A) Processing helix chain '11' and resid 565 through 569 removed outlier: 3.864A pdb=" N THR11 568 " --> pdb=" O LEU11 565 " (cutoff:3.500A) Processing helix chain '11' and resid 581 through 596 removed outlier: 3.502A pdb=" N ARG11 587 " --> pdb=" O PRO11 583 " (cutoff:3.500A) Processing helix chain '11' and resid 599 through 613 removed outlier: 3.665A pdb=" N ILE11 603 " --> pdb=" O ASP11 599 " (cutoff:3.500A) Proline residue: 11 605 - end of helix Processing helix chain '11' and resid 620 through 632 Processing helix chain '11' and resid 641 through 655 removed outlier: 3.615A pdb=" N LEU11 645 " --> pdb=" O ASN11 641 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR11 653 " --> pdb=" O CYS11 649 " (cutoff:3.500A) Processing helix chain '11' and resid 687 through 700 removed outlier: 4.385A pdb=" N MET11 700 " --> pdb=" O LEU11 696 " (cutoff:3.500A) Processing helix chain '11' and resid 705 through 730 Proline residue: 11 711 - end of helix removed outlier: 3.894A pdb=" N ARG11 714 " --> pdb=" O ASP11 710 " (cutoff:3.500A) Processing helix chain '11' and resid 733 through 747 removed outlier: 3.531A pdb=" N VAL11 737 " --> pdb=" O SER11 733 " (cutoff:3.500A) Processing helix chain '11' and resid 754 through 770 removed outlier: 3.642A pdb=" N ARG11 758 " --> pdb=" O GLY11 754 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA11 769 " --> pdb=" O ARG11 765 " (cutoff:3.500A) Processing helix chain '11' and resid 771 through 777 Processing helix chain '11' and resid 780 through 795 removed outlier: 3.889A pdb=" N THR11 786 " --> pdb=" O ASP11 782 " (cutoff:3.500A) Processing helix chain '11' and resid 806 through 820 removed outlier: 3.898A pdb=" N GLN11 810 " --> pdb=" O PRO11 806 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU11 819 " --> pdb=" O GLN11 815 " (cutoff:3.500A) Processing helix chain '11' and resid 822 through 837 removed outlier: 3.967A pdb=" N ALA11 835 " --> pdb=" O LEU11 831 " (cutoff:3.500A) Processing helix chain '11' and resid 841 through 858 Processing helix chain '11' and resid 881 through 895 Processing helix chain '11' and resid 897 through 903 Processing helix chain '11' and resid 903 through 918 removed outlier: 4.036A pdb=" N TRP11 907 " --> pdb=" O SER11 903 " (cutoff:3.500A) Processing helix chain '11' and resid 919 through 932 Processing helix chain '13' and resid 204 through 213 Processing helix chain '13' and resid 235 through 246 removed outlier: 3.725A pdb=" N ALA13 242 " --> pdb=" O ASP13 238 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR13 244 " --> pdb=" O ALA13 240 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU13 246 " --> pdb=" O ALA13 242 " (cutoff:3.500A) Processing helix chain '13' and resid 266 through 288 removed outlier: 4.014A pdb=" N LYS13 273 " --> pdb=" O ASN13 269 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE13 274 " --> pdb=" O THR13 270 " (cutoff:3.500A) Processing helix chain '14' and resid 39 through 43 removed outlier: 3.879A pdb=" N ARG14 43 " --> pdb=" O LYS14 40 " (cutoff:3.500A) Processing helix chain '14' and resid 67 through 71 removed outlier: 3.794A pdb=" N PHE14 70 " --> pdb=" O VAL14 67 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY14 71 " --> pdb=" O ASP14 68 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 67 through 71' Processing helix chain '14' and resid 76 through 87 removed outlier: 3.650A pdb=" N VAL14 80 " --> pdb=" O SER14 76 " (cutoff:3.500A) Processing helix chain '14' and resid 97 through 111 removed outlier: 4.583A pdb=" N LYS14 103 " --> pdb=" O GLN14 99 " (cutoff:3.500A) Processing helix chain '14' and resid 120 through 124 removed outlier: 3.598A pdb=" N ARG14 123 " --> pdb=" O LYS14 120 " (cutoff:3.500A) Processing helix chain '14' and resid 127 through 132 removed outlier: 4.414A pdb=" N ASP14 131 " --> pdb=" O SER14 128 " (cutoff:3.500A) Processing helix chain '14' and resid 143 through 146 Processing helix chain '14' and resid 149 through 155 removed outlier: 3.919A pdb=" N ILE14 154 " --> pdb=" O MET14 150 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR14 155 " --> pdb=" O HIS14 151 " (cutoff:3.500A) Processing helix chain '14' and resid 156 through 167 removed outlier: 4.521A pdb=" N ALA14 162 " --> pdb=" O THR14 158 " (cutoff:3.500A) Processing helix chain '14' and resid 194 through 199 Processing helix chain '14' and resid 229 through 237 removed outlier: 3.996A pdb=" N TRP14 233 " --> pdb=" O SER14 230 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARG14 234 " --> pdb=" O HIS14 231 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU14 235 " --> pdb=" O ARG14 232 " (cutoff:3.500A) Processing helix chain '14' and resid 249 through 255 Processing helix chain '14' and resid 256 through 261 removed outlier: 4.221A pdb=" N ILE14 260 " --> pdb=" O THR14 256 " (cutoff:3.500A) Processing helix chain '14' and resid 262 through 272 Processing sheet with id=AA1, first strand: chain '5' and resid 13 through 15 removed outlier: 6.685A pdb=" N ALA 5 13 " --> pdb=" O HIS 5 59 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '5' and resid 76 through 79 Processing sheet with id=AA3, first strand: chain '5' and resid 131 through 134 Processing sheet with id=AA4, first strand: chain '5' and resid 185 through 188 removed outlier: 3.771A pdb=" N VAL 5 192 " --> pdb=" O ALA 5 188 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR 5 195 " --> pdb=" O VAL 5 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 228 through 229 Processing sheet with id=AA6, first strand: chain '11' and resid 862 through 864 Processing sheet with id=AA7, first strand: chain '13' and resid 218 through 223 removed outlier: 3.727A pdb=" N PHE13 220 " --> pdb=" O GLU13 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '14' and resid 88 through 90 removed outlier: 3.521A pdb=" N THR14 209 " --> pdb=" O ILE14 287 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL14 304 " --> pdb=" O LYS14 182 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS14 310 " --> pdb=" O TYR14 176 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR14 176 " --> pdb=" O HIS14 310 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N MET14 312 " --> pdb=" O LEU14 174 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU14 174 " --> pdb=" O MET14 312 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS14 140 " --> pdb=" O VAL14 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '14' and resid 190 through 193 removed outlier: 3.986A pdb=" N TRP14 192 " --> pdb=" O PHE14 293 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N PHE14 293 " --> pdb=" O TRP14 192 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU14 226 " --> pdb=" O VAL14 275 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL14 275 " --> pdb=" O LEU14 226 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '14' and resid 322 through 323 removed outlier: 3.734A pdb=" N GLY14 322 " --> pdb=" O PHE14 331 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE14 331 " --> pdb=" O GLY14 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 1613 hydrogen bonds defined for protein. 4701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 11.31 Time building geometry restraints manager: 14.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8928 1.33 - 1.46: 5294 1.46 - 1.58: 16883 1.58 - 1.70: 186 1.70 - 1.82: 312 Bond restraints: 31603 Sorted by residual: bond pdb=" N MET10 430 " pdb=" CA MET10 430 " ideal model delta sigma weight residual 1.459 1.437 0.022 1.21e-02 6.83e+03 3.30e+00 bond pdb=" C LEU 9 844 " pdb=" N PRO 9 845 " ideal model delta sigma weight residual 1.332 1.352 -0.020 1.26e-02 6.30e+03 2.52e+00 bond pdb=" C LYS14 203 " pdb=" N PRO14 204 " ideal model delta sigma weight residual 1.328 1.346 -0.018 1.25e-02 6.40e+03 2.12e+00 bond pdb=" C ALA10 429 " pdb=" N MET10 430 " ideal model delta sigma weight residual 1.335 1.317 0.018 1.31e-02 5.83e+03 1.90e+00 bond pdb=" CG1 ILE 9 328 " pdb=" CD1 ILE 9 328 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.77e+00 ... (remaining 31598 not shown) Histogram of bond angle deviations from ideal: 97.66 - 104.94: 937 104.94 - 112.21: 16086 112.21 - 119.49: 10976 119.49 - 126.77: 14649 126.77 - 134.04: 561 Bond angle restraints: 43209 Sorted by residual: angle pdb=" N TRP10 209 " pdb=" CA TRP10 209 " pdb=" C TRP10 209 " ideal model delta sigma weight residual 114.56 109.53 5.03 1.27e+00 6.20e-01 1.57e+01 angle pdb=" CB MET11 343 " pdb=" CG MET11 343 " pdb=" SD MET11 343 " ideal model delta sigma weight residual 112.70 123.67 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CB MET11 546 " pdb=" CG MET11 546 " pdb=" SD MET11 546 " ideal model delta sigma weight residual 112.70 123.12 -10.42 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C3' U g -2 " pdb=" O3' U g -2 " pdb=" P U g -1 " ideal model delta sigma weight residual 120.20 125.40 -5.20 1.50e+00 4.44e-01 1.20e+01 angle pdb=" C TYR11 425 " pdb=" N LYS11 426 " pdb=" CA LYS11 426 " ideal model delta sigma weight residual 122.38 116.45 5.93 1.81e+00 3.05e-01 1.07e+01 ... (remaining 43204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 18354 34.99 - 69.97: 711 69.97 - 104.96: 55 104.96 - 139.94: 1 139.94 - 174.93: 9 Dihedral angle restraints: 19130 sinusoidal: 8435 harmonic: 10695 Sorted by residual: dihedral pdb=" O4' U g -4 " pdb=" C1' U g -4 " pdb=" N1 U g -4 " pdb=" C2 U g -4 " ideal model delta sinusoidal sigma weight residual 200.00 48.89 151.11 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" O4' U g -16 " pdb=" C1' U g -16 " pdb=" N1 U g -16 " pdb=" C2 U g -16 " ideal model delta sinusoidal sigma weight residual 200.00 54.33 145.67 1 1.50e+01 4.44e-03 7.79e+01 dihedral pdb=" O4' U m 124 " pdb=" C1' U m 124 " pdb=" N1 U m 124 " pdb=" C2 U m 124 " ideal model delta sinusoidal sigma weight residual 200.00 58.79 141.21 1 1.50e+01 4.44e-03 7.59e+01 ... (remaining 19127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3907 0.044 - 0.088: 887 0.088 - 0.133: 209 0.133 - 0.177: 17 0.177 - 0.221: 3 Chirality restraints: 5023 Sorted by residual: chirality pdb=" CG LEU 5 157 " pdb=" CB LEU 5 157 " pdb=" CD1 LEU 5 157 " pdb=" CD2 LEU 5 157 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C3' A m 120 " pdb=" C4' A m 120 " pdb=" O3' A m 120 " pdb=" C2' A m 120 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" CA THR 6 465 " pdb=" N THR 6 465 " pdb=" C THR 6 465 " pdb=" CB THR 6 465 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.52e-01 ... (remaining 5020 not shown) Planarity restraints: 5246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 9 443 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO 9 444 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO 9 444 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO 9 444 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU 9 74 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO 9 75 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO 9 75 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO 9 75 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG11 873 " -0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO11 874 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO11 874 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO11 874 " -0.024 5.00e-02 4.00e+02 ... (remaining 5243 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2821 2.74 - 3.28: 32942 3.28 - 3.82: 51780 3.82 - 4.36: 58171 4.36 - 4.90: 96714 Nonbonded interactions: 242428 Sorted by model distance: nonbonded pdb=" O GLN 9 325 " pdb=" OG SER 9 329 " model vdw 2.198 2.440 nonbonded pdb=" O SER 8 353 " pdb=" OG SER 8 353 " model vdw 2.201 2.440 nonbonded pdb=" O GLU 9 141 " pdb=" OG SER 9 145 " model vdw 2.207 2.440 nonbonded pdb=" OE2 GLU 6 200 " pdb=" OG1 THR10 337 " model vdw 2.208 2.440 nonbonded pdb=" O PHE 5 187 " pdb=" OG SER 5 230 " model vdw 2.209 2.440 ... (remaining 242423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.400 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: 0.020 Extract box with map and model: 24.480 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 90.020 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31603 Z= 0.189 Angle : 0.603 10.968 43209 Z= 0.318 Chirality : 0.039 0.221 5023 Planarity : 0.004 0.056 5246 Dihedral : 17.776 174.930 12164 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.32 % Allowed : 24.16 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3622 helix: 1.01 (0.11), residues: 2212 sheet: -1.18 (0.40), residues: 140 loop : -0.76 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 7 112 HIS 0.008 0.001 HIS13 206 PHE 0.027 0.001 PHE 5 42 TYR 0.015 0.001 TYR11 418 ARG 0.009 0.000 ARG10 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 239 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 246 average time/residue: 0.3358 time to fit residues: 139.7317 Evaluate side-chains 227 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 2.572 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2160 time to fit residues: 4.1872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 312 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 189 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 176 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 336 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: