Starting phenix.real_space_refine (version: dev) on Tue May 17 05:23:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqu_20170/05_2022/6oqu_20170_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqu_20170/05_2022/6oqu_20170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqu_20170/05_2022/6oqu_20170.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqu_20170/05_2022/6oqu_20170.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqu_20170/05_2022/6oqu_20170_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqu_20170/05_2022/6oqu_20170_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 36971 Number of models: 1 Model: "" Number of chains: 28 Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 493, 'PCIS': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3871 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 494, 'PCIS': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3832 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 489, 'PCIS': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1034 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 7, 'TRANS': 274, 'PCIS': 2} Chain: "F" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 19, 'TRANS': 437, 'PCIS': 1} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 19, 'TRANS': 439, 'PCIS': 1} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 19, 'TRANS': 439, 'PCIS': 1} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 14, 'TRANS': 250, 'PCIS': 1} Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'PO4': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 20.06, per 1000 atoms: 0.54 Number of scatterers: 36971 At special positions: 0 Unit cell: (176.956, 220.116, 139.191, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 180 16.00 P 16 15.00 Mg 5 11.99 O 6968 8.00 N 6317 7.00 C 23485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.00 Conformation dependent library (CDL) restraints added in 5.7 seconds 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 179 helices and 25 sheets defined 55.7% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'W' and resid 6 through 20 removed outlier: 4.686A pdb=" N TYR W 10 " --> pdb=" O VAL W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.813A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 48 removed outlier: 3.688A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 63 removed outlier: 4.047A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 82 removed outlier: 4.014A pdb=" N LEU W 75 " --> pdb=" O ASN W 71 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE W 76 " --> pdb=" O GLY W 72 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN W 82 " --> pdb=" O VAL W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 102 Proline residue: W 89 - end of helix removed outlier: 3.970A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN W 94 " --> pdb=" O VAL W 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 131 removed outlier: 4.518A pdb=" N GLU W 129 " --> pdb=" O SER W 125 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS W 130 " --> pdb=" O ALA W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 163 through 168 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 175 through 188 removed outlier: 3.924A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASP C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 3.631A pdb=" N ASN C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.957A pdb=" N ALA C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.632A pdb=" N MET C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.250A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 342 through 348 removed outlier: 4.009A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 removed outlier: 3.748A pdb=" N ALA C 362 " --> pdb=" O ASN C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 412 removed outlier: 3.813A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLN C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N SER C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 430 removed outlier: 3.645A pdb=" N LYS C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 477 removed outlier: 3.512A pdb=" N ILE C 464 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL C 475 " --> pdb=" O LEU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.652A pdb=" N GLN C 488 " --> pdb=" O GLN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'B' and resid 5 through 17 removed outlier: 4.053A pdb=" N ARG B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.673A pdb=" N ALA B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 removed outlier: 3.611A pdb=" N ARG B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.740A pdb=" N MET B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 removed outlier: 3.668A pdb=" N ALA B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.320A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 293 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 340 through 346 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 384 through 390 Processing helix chain 'B' and resid 393 through 408 removed outlier: 3.634A pdb=" N GLU B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 431 removed outlier: 3.533A pdb=" N LYS B 426 " --> pdb=" O ASP B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 464 through 478 removed outlier: 3.672A pdb=" N ALA B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 486 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 188 removed outlier: 4.008A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 251 Proline residue: A 239 - end of helix removed outlier: 3.585A pdb=" N MET A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 4.078A pdb=" N VAL A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.607A pdb=" N ARG A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 340 through 347 removed outlier: 3.566A pdb=" N SER A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 409 removed outlier: 3.637A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N THR A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 removed outlier: 3.645A pdb=" N LYS A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.375A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.583A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 22 removed outlier: 4.014A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE X 12 " --> pdb=" O GLY X 9 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE X 14 " --> pdb=" O ALA X 11 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU X 16 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA X 21 " --> pdb=" O VAL X 18 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 135 removed outlier: 3.813A pdb=" N ILE X 33 " --> pdb=" O LEU X 29 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU X 39 " --> pdb=" O LYS X 35 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP X 42 " --> pdb=" O LYS X 38 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN X 64 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU X 65 " --> pdb=" O ALA X 61 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS X 66 " --> pdb=" O THR X 62 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA X 70 " --> pdb=" O LYS X 66 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU X 71 " --> pdb=" O LYS X 67 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA X 92 " --> pdb=" O ASP X 88 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 155 removed outlier: 3.822A pdb=" N SER X 146 " --> pdb=" O ALA X 143 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASP X 147 " --> pdb=" O ALA X 144 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP X 150 " --> pdb=" O ASP X 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 102 removed outlier: 3.610A pdb=" N ARG H 93 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU H 102 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 130 through 133 No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'G' and resid 3 through 57 removed outlier: 3.879A pdb=" N SER G 8 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA G 39 " --> pdb=" O GLN G 35 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 90 through 108 removed outlier: 3.958A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 removed outlier: 3.683A pdb=" N SER G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 160 removed outlier: 4.397A pdb=" N GLY G 150 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Proline residue: G 151 - end of helix removed outlier: 3.775A pdb=" N VAL G 154 " --> pdb=" O PRO G 151 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP G 160 " --> pdb=" O GLN G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 202 removed outlier: 3.964A pdb=" N LYS G 201 " --> pdb=" O LEU G 198 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 202' Processing helix chain 'G' and resid 211 through 282 removed outlier: 3.551A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 116 through 118 No H-bonds generated for 'chain 'F' and resid 116 through 118' Processing helix chain 'F' and resid 131 through 136 Processing helix chain 'F' and resid 157 through 168 removed outlier: 4.011A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 196 removed outlier: 3.742A pdb=" N PHE F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 213 through 232 removed outlier: 4.998A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.636A pdb=" N GLU F 253 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 279 removed outlier: 3.729A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 306 through 314 removed outlier: 4.710A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 removed outlier: 4.878A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 377 removed outlier: 7.294A pdb=" N GLN F 351 " --> pdb=" O LEU F 347 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N GLU F 352 " --> pdb=" O VAL F 348 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HIS F 353 " --> pdb=" O VAL F 349 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS F 371 " --> pdb=" O TYR F 367 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 381 No H-bonds generated for 'chain 'F' and resid 379 through 381' Processing helix chain 'F' and resid 384 through 399 removed outlier: 3.760A pdb=" N LEU F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG F 398 " --> pdb=" O ARG F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 411 Processing helix chain 'F' and resid 421 through 431 removed outlier: 3.893A pdb=" N GLY F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS F 428 " --> pdb=" O ILE F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 449 through 455 Processing helix chain 'E' and resid 19 through 21 No H-bonds generated for 'chain 'E' and resid 19 through 21' Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 155 through 168 Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.657A pdb=" N GLU E 192 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 213 through 233 removed outlier: 5.176A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.537A pdb=" N GLY E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 306 through 311 Processing helix chain 'E' and resid 323 through 327 Processing helix chain 'E' and resid 346 through 349 No H-bonds generated for 'chain 'E' and resid 346 through 349' Processing helix chain 'E' and resid 351 through 377 removed outlier: 4.064A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 386 through 399 removed outlier: 3.754A pdb=" N ALA E 391 " --> pdb=" O LYS E 387 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG E 394 " --> pdb=" O VAL E 390 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 420 through 432 removed outlier: 3.722A pdb=" N GLU E 432 " --> pdb=" O LYS E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'E' and resid 452 through 456 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 155 through 169 Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 198 through 201 Processing helix chain 'D' and resid 213 through 232 removed outlier: 5.014A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 257 Processing helix chain 'D' and resid 271 through 279 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 306 through 313 removed outlier: 3.726A pdb=" N THR D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 346 through 377 removed outlier: 7.233A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N GLU D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS D 353 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 384 through 399 removed outlier: 3.847A pdb=" N LEU D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 411 removed outlier: 3.600A pdb=" N THR D 411 " --> pdb=" O GLU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 431 removed outlier: 3.514A pdb=" N GLY D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 442 No H-bonds generated for 'chain 'D' and resid 440 through 442' Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.688A pdb=" N VAL D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 41 removed outlier: 4.277A pdb=" N TYR J 10 " --> pdb=" O MET J 6 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N MET J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET J 16 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 77 removed outlier: 3.740A pdb=" N GLY J 58 " --> pdb=" O PHE J 54 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'L' and resid 4 through 41 removed outlier: 3.871A pdb=" N MET L 11 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA L 14 " --> pdb=" O TYR L 10 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 removed outlier: 3.699A pdb=" N ILE L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Proline residue: L 47 - end of helix removed outlier: 4.506A pdb=" N GLY L 58 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA L 62 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix Processing helix chain 'M' and resid 5 through 41 removed outlier: 3.937A pdb=" N LEU M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 76 Proline residue: M 47 - end of helix removed outlier: 4.071A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP M 61 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.200A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 Proline residue: N 47 - end of helix removed outlier: 3.513A pdb=" N VAL N 56 " --> pdb=" O PHE N 53 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY N 58 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP N 61 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix removed outlier: 3.686A pdb=" N VAL N 68 " --> pdb=" O MET N 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 41 removed outlier: 3.753A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET O 11 " --> pdb=" O ASP O 7 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.692A pdb=" N PHE O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 76 removed outlier: 3.546A pdb=" N ILE O 66 " --> pdb=" O ALA O 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 41 removed outlier: 4.132A pdb=" N ALA P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 77 removed outlier: 3.706A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix Processing helix chain 'Q' and resid 4 through 39 removed outlier: 4.482A pdb=" N LEU Q 9 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA Q 20 " --> pdb=" O MET Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 3.886A pdb=" N PHE Q 54 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.737A pdb=" N ALA Q 67 " --> pdb=" O PRO Q 64 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL Q 68 " --> pdb=" O MET Q 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.764A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU R 9 " --> pdb=" O ASN R 5 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR R 10 " --> pdb=" O MET R 6 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET R 11 " --> pdb=" O ASP R 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 76 removed outlier: 3.711A pdb=" N VAL R 56 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'Y' and resid 3 through 24 removed outlier: 3.528A pdb=" N PHE Y 20 " --> pdb=" O LEU Y 16 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 59 removed outlier: 3.603A pdb=" N GLY Y 43 " --> pdb=" O GLU Y 39 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA Y 47 " --> pdb=" O GLY Y 43 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS Y 52 " --> pdb=" O GLU Y 48 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP Y 53 " --> pdb=" O ARG Y 49 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASP Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS Y 58 " --> pdb=" O LEU Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 61 through 101 removed outlier: 3.936A pdb=" N ILE Y 76 " --> pdb=" O ALA Y 72 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA Y 94 " --> pdb=" O ALA Y 90 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN Y 96 " --> pdb=" O ALA Y 92 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 138 removed outlier: 3.864A pdb=" N ALA Y 107 " --> pdb=" O GLN Y 104 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE Y 109 " --> pdb=" O GLN Y 106 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA Y 111 " --> pdb=" O GLU Y 108 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU Y 133 " --> pdb=" O ALA Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 155 removed outlier: 3.502A pdb=" N ALA Y 154 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU Y 155 " --> pdb=" O LYS Y 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 16 removed outlier: 3.660A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS a 15 " --> pdb=" O TYR a 11 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 66 removed outlier: 3.616A pdb=" N PHE a 48 " --> pdb=" O ASP a 44 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL a 50 " --> pdb=" O MET a 46 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU a 59 " --> pdb=" O LEU a 55 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LYS a 66 " --> pdb=" O SER a 62 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 93 removed outlier: 4.400A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE a 79 " --> pdb=" O PHE a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 99 through 120 removed outlier: 3.813A pdb=" N ALA a 102 " --> pdb=" O LYS a 99 " (cutoff:3.500A) Proline residue: a 103 - end of helix removed outlier: 3.591A pdb=" N TRP a 111 " --> pdb=" O ILE a 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL a 112 " --> pdb=" O PHE a 109 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET a 118 " --> pdb=" O MET a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 133 removed outlier: 3.636A pdb=" N GLU a 131 " --> pdb=" O PRO a 127 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS a 132 " --> pdb=" O TYR a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 143 through 145 No H-bonds generated for 'chain 'a' and resid 143 through 145' Processing helix chain 'a' and resid 147 through 167 removed outlier: 3.907A pdb=" N LEU a 160 " --> pdb=" O GLY a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 180 removed outlier: 4.005A pdb=" N PHE a 174 " --> pdb=" O GLY a 170 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 228 Proline residue: a 190 - end of helix removed outlier: 3.793A pdb=" N LEU a 193 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE a 194 " --> pdb=" O VAL a 191 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.578A pdb=" N LEU a 209 " --> pdb=" O SER a 206 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY a 213 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN a 214 " --> pdb=" O LEU a 211 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA a 217 " --> pdb=" O ASN a 214 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU a 220 " --> pdb=" O ALA a 217 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU a 228 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 3.532A pdb=" N GLN a 234 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TRP a 235 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU a 237 " --> pdb=" O GLN a 234 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL a 239 " --> pdb=" O ILE a 236 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 4.164A pdb=" N ILE a 255 " --> pdb=" O GLN a 252 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER a 265 " --> pdb=" O VAL a 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 7 No H-bonds generated for 'chain 'I' and resid 4 through 7' Processing helix chain 'I' and resid 9 through 41 removed outlier: 3.580A pdb=" N ILE I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 76 Proline residue: I 47 - end of helix removed outlier: 4.675A pdb=" N GLY I 58 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL I 60 " --> pdb=" O MET I 57 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.620A pdb=" N ALA I 67 " --> pdb=" O PRO I 64 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU I 70 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR I 73 " --> pdb=" O LEU I 70 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL I 74 " --> pdb=" O GLY I 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 41 Processing helix chain 'S' and resid 43 through 75 Proline residue: S 47 - end of helix removed outlier: 3.600A pdb=" N ARG S 50 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE S 55 " --> pdb=" O GLN S 52 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY S 58 " --> pdb=" O ILE S 55 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP S 61 " --> pdb=" O GLY S 58 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE S 63 " --> pdb=" O VAL S 60 " (cutoff:3.500A) Proline residue: S 64 - end of helix removed outlier: 3.918A pdb=" N LEU S 70 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU S 72 " --> pdb=" O GLY S 69 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL S 74 " --> pdb=" O GLY S 71 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'W' and resid 135 through 142 removed outlier: 3.644A pdb=" N VAL W 110 " --> pdb=" O ASN W 139 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.564A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= D, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.450A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N CYS C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL C 224 " --> pdb=" O CYS C 193 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU C 327 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 352 through 355 removed outlier: 6.648A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.457A pdb=" N ASN B 27 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= H, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.581A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 169 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 221 through 226 removed outlier: 8.783A pdb=" N ILE B 222 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N VAL B 224 " --> pdb=" O CYS B 193 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP B 255 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE B 194 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B 257 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL B 196 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE B 259 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 198 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.520A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= L, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.672A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 221 through 226 removed outlier: 6.882A pdb=" N CYS A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL A 224 " --> pdb=" O CYS A 193 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A 327 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.065A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 180 through 188 removed outlier: 6.596A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 4 through 9 removed outlier: 6.499A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.805A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 317 through 320 removed outlier: 7.887A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL F 296 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 4 through 9 removed outlier: 6.347A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.773A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 317 through 319 removed outlier: 3.536A pdb=" N GLY E 146 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR E 173 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N PHE E 240 " --> pdb=" O TYR E 173 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL E 175 " --> pdb=" O PHE E 240 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.674A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= X, first strand: chain 'D' and resid 317 through 320 removed outlier: 8.798A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'a' and resid 20 through 22 removed outlier: 4.483A pdb=" N GLN a 20 " --> pdb=" O VAL a 29 " (cutoff:3.500A) 1876 hydrogen bonds defined for protein. 4716 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: 13.71 Time building geometry restraints manager: 17.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 6333 1.29 - 1.42: 8600 1.42 - 1.55: 22211 1.55 - 1.68: 24 1.68 - 1.81: 360 Bond restraints: 37528 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.20e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.15e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.91e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.83e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.38e+01 ... (remaining 37523 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.48: 814 105.48 - 113.16: 20943 113.16 - 120.85: 18571 120.85 - 128.53: 10255 128.53 - 136.21: 214 Bond angle restraints: 50797 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 115.95 23.92 1.00e+00 1.00e+00 5.72e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 116.84 23.03 1.00e+00 1.00e+00 5.31e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.91 21.96 1.00e+00 1.00e+00 4.82e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.85 19.98 1.00e+00 1.00e+00 3.99e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 119.58 17.25 1.00e+00 1.00e+00 2.97e+02 ... (remaining 50792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.97: 21961 30.97 - 61.95: 653 61.95 - 92.92: 82 92.92 - 123.90: 2 123.90 - 154.87: 3 Dihedral angle restraints: 22701 sinusoidal: 8917 harmonic: 13784 Sorted by residual: dihedral pdb=" C ASP C 261 " pdb=" N ASP C 261 " pdb=" CA ASP C 261 " pdb=" CB ASP C 261 " ideal model delta harmonic sigma weight residual -122.60 -145.64 23.04 0 2.50e+00 1.60e-01 8.49e+01 dihedral pdb=" N ASP C 261 " pdb=" C ASP C 261 " pdb=" CA ASP C 261 " pdb=" CB ASP C 261 " ideal model delta harmonic sigma weight residual 122.80 145.59 -22.79 0 2.50e+00 1.60e-01 8.31e+01 dihedral pdb=" O1B ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PB ADP D 500 " pdb=" PA ADP D 500 " ideal model delta sinusoidal sigma weight residual 300.00 145.12 154.87 1 2.00e+01 2.50e-03 4.57e+01 ... (remaining 22698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 5897 0.197 - 0.394: 20 0.394 - 0.591: 2 0.591 - 0.789: 0 0.789 - 0.986: 1 Chirality restraints: 5920 Sorted by residual: chirality pdb=" CA ASP C 261 " pdb=" N ASP C 261 " pdb=" C ASP C 261 " pdb=" CB ASP C 261 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" CA LEU a 178 " pdb=" N LEU a 178 " pdb=" C LEU a 178 " pdb=" CB LEU a 178 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CA ASP C 262 " pdb=" N ASP C 262 " pdb=" C ASP C 262 " pdb=" CB ASP C 262 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.50e+00 ... (remaining 5917 not shown) Planarity restraints: 6550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA I 14 " -0.022 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C ALA I 14 " 0.080 2.00e-02 2.50e+03 pdb=" O ALA I 14 " -0.030 2.00e-02 2.50e+03 pdb=" N VAL I 15 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 264 " 0.022 2.00e-02 2.50e+03 4.53e-02 2.06e+01 pdb=" C ALA D 264 " -0.078 2.00e-02 2.50e+03 pdb=" O ALA D 264 " 0.028 2.00e-02 2.50e+03 pdb=" N VAL D 265 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 5 " 0.020 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C ASN L 5 " -0.072 2.00e-02 2.50e+03 pdb=" O ASN L 5 " 0.027 2.00e-02 2.50e+03 pdb=" N MET L 6 " 0.025 2.00e-02 2.50e+03 ... (remaining 6547 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 46 2.35 - 2.99: 21951 2.99 - 3.63: 53499 3.63 - 4.26: 84899 4.26 - 4.90: 143932 Nonbonded interactions: 304327 Sorted by model distance: nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.718 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.749 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.811 2.170 nonbonded pdb=" OG1 THR F 156 " pdb="MG MG F 501 " model vdw 1.833 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.848 2.170 ... (remaining 304322 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) selection = (chain 'B' and (resid 4 through 511 or resid 600 through 601)) selection = (chain 'C' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 459 or resid 500)) selection = (chain 'E' and (resid 2 through 459 or resid 500)) selection = (chain 'F' and (resid 2 through 459 or resid 500)) } ncs_group { reference = (chain 'I' and resid 3 through 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 180 5.16 5 C 23485 2.51 5 N 6317 2.21 5 O 6968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 0.040 Extract box with map and model: 12.600 Check model and map are aligned: 0.510 Convert atoms to be neutral: 0.350 Process input model: 93.140 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 : 0.009 0.113 37528 Z= 0.605 Angle : 0.927 23.924 50797 Z= 0.615 Chirality : 0.054 0.986 5920 Planarity : 0.005 0.055 6550 Dihedral : 14.947 154.874 13883 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.03 % 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: -2.70 (0.10), residues: 4807 helix: -1.84 (0.08), residues: 2579 sheet: -0.92 (0.19), residues: 564 loop : -1.67 (0.14), residues: 1664 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 761 time to evaluate : 4.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 68 residues processed: 859 average time/residue: 0.5061 time to fit residues: 694.1139 Evaluate side-chains 649 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 581 time to evaluate : 5.067 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.3400 time to fit residues: 49.9528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 5.9990 chunk 358 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 241 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 370 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 429 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 71 ASN W 94 GLN C 369 ASN B 26 HIS B 186 GLN B 408 GLN A 65 ASN A 147 GLN A 408 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 145 ASN H 14 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN G 274 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 GLN F 353 HIS F 437 HIS E 441 GLN D 73 HIS D 170 HIS D 437 HIS J 52 GLN L 3 ASN L 5 ASN M 5 ASN N 3 ASN O 3 ASN P 3 ASN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 HIS ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 37528 Z= 0.201 Angle : 0.631 11.267 50797 Z= 0.327 Chirality : 0.044 0.346 5920 Planarity : 0.005 0.144 6550 Dihedral : 6.597 143.398 5248 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: -0.99 (0.11), residues: 4807 helix: -0.36 (0.10), residues: 2625 sheet: -0.53 (0.21), residues: 520 loop : -0.91 (0.15), residues: 1662 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 646 time to evaluate : 4.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 31 residues processed: 705 average time/residue: 0.4879 time to fit residues: 559.8158 Evaluate side-chains 620 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 589 time to evaluate : 3.971 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3706 time to fit residues: 26.4877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 238 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 357 optimal weight: 2.9990 chunk 292 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 430 optimal weight: 0.8980 chunk 464 optimal weight: 6.9990 chunk 383 optimal weight: 10.0000 chunk 426 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 345 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN B 147 GLN B 399 GLN A 358 ASN ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 GLN G 274 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN L 3 ASN L 5 ASN Y 10 GLN ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 ASN S 42 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 37528 Z= 0.288 Angle : 0.620 8.453 50797 Z= 0.317 Chirality : 0.044 0.237 5920 Planarity : 0.005 0.122 6550 Dihedral : 6.172 151.437 5248 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: -0.53 (0.12), residues: 4807 helix: 0.04 (0.10), residues: 2631 sheet: -0.34 (0.22), residues: 514 loop : -0.76 (0.15), residues: 1662 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 614 time to evaluate : 4.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 46 residues processed: 676 average time/residue: 0.5190 time to fit residues: 577.3340 Evaluate side-chains 616 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 570 time to evaluate : 4.259 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.3518 time to fit residues: 36.0165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 425 optimal weight: 9.9990 chunk 323 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 288 optimal weight: 0.4980 chunk 431 optimal weight: 0.9990 chunk 457 optimal weight: 4.9990 chunk 225 optimal weight: 0.5980 chunk 409 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN X 78 GLN H 24 GLN G 274 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 37528 Z= 0.204 Angle : 0.577 8.453 50797 Z= 0.294 Chirality : 0.042 0.264 5920 Planarity : 0.004 0.077 6550 Dihedral : 5.867 150.180 5248 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: -0.18 (0.12), residues: 4807 helix: 0.35 (0.10), residues: 2623 sheet: -0.26 (0.22), residues: 520 loop : -0.63 (0.15), residues: 1664 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 613 time to evaluate : 4.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 32 residues processed: 660 average time/residue: 0.5080 time to fit residues: 548.2715 Evaluate side-chains 606 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 574 time to evaluate : 4.517 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3511 time to fit residues: 26.9137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 380 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 340 optimal weight: 4.9990 chunk 188 optimal weight: 0.3980 chunk 390 optimal weight: 0.0970 chunk 316 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 233 optimal weight: 0.0050 chunk 410 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN X 37 GLN X 78 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 GLN L 5 ASN R 52 GLN ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 ASN a 20 GLN ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.071 37528 Z= 0.151 Angle : 0.556 8.808 50797 Z= 0.281 Chirality : 0.041 0.235 5920 Planarity : 0.004 0.060 6550 Dihedral : 5.471 146.501 5248 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.17 (0.12), residues: 4807 helix: 0.64 (0.10), residues: 2611 sheet: -0.10 (0.22), residues: 516 loop : -0.48 (0.15), residues: 1680 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 622 time to evaluate : 5.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 18 residues processed: 654 average time/residue: 0.5135 time to fit residues: 547.0210 Evaluate side-chains 595 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 577 time to evaluate : 4.329 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3667 time to fit residues: 17.8213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 153 optimal weight: 4.9990 chunk 411 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 268 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 457 optimal weight: 0.9980 chunk 379 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN B 399 GLN X 64 GLN ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 HIS ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 GLN M 52 GLN ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 145 ASN a 76 GLN a 234 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 37528 Z= 0.188 Angle : 0.572 10.800 50797 Z= 0.287 Chirality : 0.042 0.220 5920 Planarity : 0.004 0.050 6550 Dihedral : 5.391 148.553 5248 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.32 (0.12), residues: 4807 helix: 0.77 (0.10), residues: 2615 sheet: -0.08 (0.22), residues: 529 loop : -0.42 (0.15), residues: 1663 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 593 time to evaluate : 4.508 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 18 residues processed: 623 average time/residue: 0.4983 time to fit residues: 505.8912 Evaluate side-chains 589 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 571 time to evaluate : 4.233 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3752 time to fit residues: 17.9352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 441 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 260 optimal weight: 0.6980 chunk 334 optimal weight: 3.9990 chunk 258 optimal weight: 20.0000 chunk 385 optimal weight: 1.9990 chunk 255 optimal weight: 0.0070 chunk 455 optimal weight: 1.9990 chunk 285 optimal weight: 9.9990 chunk 277 optimal weight: 0.0370 chunk 210 optimal weight: 10.0000 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN A 123 HIS ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 GLN R 52 GLN ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 37528 Z= 0.161 Angle : 0.572 11.393 50797 Z= 0.285 Chirality : 0.041 0.225 5920 Planarity : 0.004 0.062 6550 Dihedral : 5.191 147.122 5248 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.47 (0.12), residues: 4807 helix: 0.89 (0.10), residues: 2603 sheet: 0.04 (0.22), residues: 525 loop : -0.35 (0.15), residues: 1679 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 604 time to evaluate : 4.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 15 residues processed: 626 average time/residue: 0.5041 time to fit residues: 517.8823 Evaluate side-chains 587 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 572 time to evaluate : 4.459 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3401 time to fit residues: 15.5810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 282 optimal weight: 0.3980 chunk 182 optimal weight: 10.0000 chunk 272 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 289 optimal weight: 0.0670 chunk 310 optimal weight: 7.9990 chunk 225 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 358 optimal weight: 0.0770 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN B 399 GLN ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN F 7 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 ASN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 37528 Z= 0.158 Angle : 0.588 17.518 50797 Z= 0.289 Chirality : 0.041 0.188 5920 Planarity : 0.004 0.066 6550 Dihedral : 5.012 144.014 5248 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.57 (0.12), residues: 4807 helix: 0.97 (0.10), residues: 2600 sheet: 0.12 (0.23), residues: 511 loop : -0.32 (0.15), residues: 1696 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 592 time to evaluate : 4.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 606 average time/residue: 0.5234 time to fit residues: 517.1423 Evaluate side-chains 574 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 569 time to evaluate : 4.415 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3282 time to fit residues: 9.0832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 414 optimal weight: 10.0000 chunk 436 optimal weight: 2.9990 chunk 398 optimal weight: 4.9990 chunk 424 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 333 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 383 optimal weight: 7.9990 chunk 401 optimal weight: 0.0670 chunk 423 optimal weight: 5.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 73 GLN W 94 GLN ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 HIS ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.099 37528 Z= 0.250 Angle : 0.618 15.005 50797 Z= 0.307 Chirality : 0.043 0.229 5920 Planarity : 0.005 0.140 6550 Dihedral : 5.124 149.377 5248 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.50 (0.12), residues: 4807 helix: 0.92 (0.10), residues: 2615 sheet: 0.06 (0.22), residues: 528 loop : -0.37 (0.15), residues: 1664 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 574 time to evaluate : 4.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 579 average time/residue: 0.5239 time to fit residues: 493.6946 Evaluate side-chains 573 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 564 time to evaluate : 4.297 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3289 time to fit residues: 10.9869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 278 optimal weight: 4.9990 chunk 449 optimal weight: 9.9990 chunk 274 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 312 optimal weight: 0.4980 chunk 471 optimal weight: 0.8980 chunk 433 optimal weight: 0.9980 chunk 375 optimal weight: 0.0060 chunk 38 optimal weight: 0.7980 chunk 289 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN F 7 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 GLN ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.102 37528 Z= 0.167 Angle : 0.607 14.992 50797 Z= 0.300 Chirality : 0.042 0.278 5920 Planarity : 0.004 0.113 6550 Dihedral : 4.998 146.734 5248 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.61 (0.12), residues: 4807 helix: 1.00 (0.11), residues: 2609 sheet: 0.19 (0.22), residues: 521 loop : -0.32 (0.15), residues: 1677 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 592 time to evaluate : 4.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 594 average time/residue: 0.5211 time to fit residues: 502.7546 Evaluate side-chains 576 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 571 time to evaluate : 4.288 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3447 time to fit residues: 9.0319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 298 optimal weight: 8.9990 chunk 399 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 345 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 375 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 385 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN B 399 GLN ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 GLN F 7 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.067591 restraints weight = 78307.261| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.01 r_work: 0.2874 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 1.79 restraints_weight: 0.2500 r_work: 0.2851 rms_B_bonded: 1.82 restraints_weight: 0.1250 r_work: 0.2839 rms_B_bonded: 1.90 restraints_weight: 0.0625 r_work: 0.2826 rms_B_bonded: 2.01 restraints_weight: 0.0312 r_work: 0.2812 rms_B_bonded: 2.15 restraints_weight: 0.0156 r_work: 0.2796 rms_B_bonded: 2.33 restraints_weight: 0.0078 r_work: 0.2780 rms_B_bonded: 2.55 restraints_weight: 0.0039 r_work: 0.2762 rms_B_bonded: 2.81 restraints_weight: 0.0020 r_work: 0.2742 rms_B_bonded: 3.11 restraints_weight: 0.0010 r_work: 0.2721 rms_B_bonded: 3.46 restraints_weight: 0.0005 r_work: 0.2697 rms_B_bonded: 3.87 restraints_weight: 0.0002 r_work: 0.2671 rms_B_bonded: 4.35 restraints_weight: 0.0001 r_work: 0.2643 rms_B_bonded: 4.89 restraints_weight: 0.0001 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 37528 Z= 0.306 Angle : 0.648 16.646 50797 Z= 0.323 Chirality : 0.044 0.265 5920 Planarity : 0.005 0.135 6550 Dihedral : 5.207 153.125 5248 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.51 (0.12), residues: 4807 helix: 0.92 (0.10), residues: 2621 sheet: 0.13 (0.22), residues: 520 loop : -0.39 (0.15), residues: 1666 =============================================================================== Job complete usr+sys time: 9300.76 seconds wall clock time: 167 minutes 46.02 seconds (10066.02 seconds total)