Starting phenix.real_space_refine on Sat Aug 10 12:04:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/08_2024/6oa9_0665_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/08_2024/6oa9_0665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/08_2024/6oa9_0665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/08_2024/6oa9_0665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/08_2024/6oa9_0665_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/08_2024/6oa9_0665_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.017 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 29 5.49 5 S 129 5.16 5 C 18142 2.51 5 N 5035 2.21 5 O 5669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ASP 324": "OD1" <-> "OD2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A ARG 609": "NH1" <-> "NH2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 776": "NH1" <-> "NH2" Residue "A ARG 788": "NH1" <-> "NH2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 348": "NH1" <-> "NH2" Residue "B PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B ASP 487": "OD1" <-> "OD2" Residue "B TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 609": "NH1" <-> "NH2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ARG 227": "NH1" <-> "NH2" Residue "C ARG 235": "NH1" <-> "NH2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 348": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "C ASP 378": "OD1" <-> "OD2" Residue "C TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C ARG 596": "NH1" <-> "NH2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C ASP 650": "OD1" <-> "OD2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 348": "NH1" <-> "NH2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D ARG 392": "NH1" <-> "NH2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D ASP 487": "OD1" <-> "OD2" Residue "D TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "D PHE 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 648": "NH1" <-> "NH2" Residue "D TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 717": "NH1" <-> "NH2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "E ASP 324": "OD1" <-> "OD2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 392": "NH1" <-> "NH2" Residue "E GLU 504": "OE1" <-> "OE2" Residue "E TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 596": "NH1" <-> "NH2" Residue "E TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 210": "OE1" <-> "OE2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "F ARG 297": "NH1" <-> "NH2" Residue "F PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 323": "NH1" <-> "NH2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F ARG 348": "NH1" <-> "NH2" Residue "F ARG 392": "NH1" <-> "NH2" Residue "F ASP 405": "OD1" <-> "OD2" Residue "F GLU 476": "OE1" <-> "OE2" Residue "F GLU 480": "OE1" <-> "OE2" Residue "F GLU 504": "OE1" <-> "OE2" Residue "F TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 574": "OD1" <-> "OD2" Residue "F ARG 609": "NH1" <-> "NH2" Residue "F ARG 645": "NH1" <-> "NH2" Residue "F PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 776": "NH1" <-> "NH2" Residue "F TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K ASP 39": "OD1" <-> "OD2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 242": "NH1" <-> "NH2" Residue "J TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "G ASP 141": "OD1" <-> "OD2" Residue "G ARG 142": "NH1" <-> "NH2" Residue "G PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G GLU 209": "OE1" <-> "OE2" Residue "G GLU 230": "OE1" <-> "OE2" Residue "G PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 312": "NH1" <-> "NH2" Residue "G ARG 321": "NH1" <-> "NH2" Residue "G PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 364": "NH1" <-> "NH2" Residue "G PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 404": "OE1" <-> "OE2" Residue "G GLU 406": "OE1" <-> "OE2" Residue "G ASP 430": "OD1" <-> "OD2" Residue "G ARG 432": "NH1" <-> "NH2" Residue "G PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 474": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29006 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4206 Classifications: {'peptide': 547} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 518} Chain breaks: 1 Chain: "B" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3767 Classifications: {'peptide': 493} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 3759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3759 Classifications: {'peptide': 492} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 464} Chain breaks: 1 Chain: "D" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3747 Classifications: {'peptide': 489} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 461} Chain breaks: 1 Chain: "E" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3786 Classifications: {'peptide': 496} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 468} Chain breaks: 1 Chain: "F" Number of atoms: 4093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4093 Classifications: {'peptide': 533} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 505} Chain breaks: 2 Chain: "K" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "H" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "J" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "G" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3762 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 447} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'ATP': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25196 SG CYS G 145 47.953 81.487 84.359 1.00137.84 S ATOM 25812 SG CYS G 219 71.508 37.375 89.822 1.00142.70 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N LEU H 173 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU H 173 " occ=0.45 residue: pdb=" N ARG H 174 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG H 174 " occ=0.45 residue: pdb=" N GLY H 175 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY H 175 " occ=0.25 residue: pdb=" N GLY H 176 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY H 176 " occ=0.25 residue: pdb=" N LEU J 273 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU J 273 " occ=0.45 residue: pdb=" N ARG J 274 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG J 274 " occ=0.45 residue: pdb=" N GLY J 275 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY J 275 " occ=0.25 residue: pdb=" N GLY J 276 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY J 276 " occ=0.25 Time building chain proxies: 15.27, per 1000 atoms: 0.53 Number of scatterers: 29006 At special positions: 0 Unit cell: (144.45, 140.4, 178.2, 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) Zn 2 29.99 S 129 16.00 P 29 15.00 O 5669 8.00 N 5035 7.00 C 18142 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.27 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 139 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 145 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 219 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 208 " 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6870 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 18 sheets defined 40.9% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 219 through 236 removed outlier: 3.663A pdb=" N GLN A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.717A pdb=" N LYS A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.562A pdb=" N GLU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.911A pdb=" N MET A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 306 removed outlier: 3.581A pdb=" N SER A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.950A pdb=" N ILE A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 removed outlier: 3.806A pdb=" N ARG A 332 " --> pdb=" O GLU A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.507A pdb=" N ARG A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 395 removed outlier: 3.547A pdb=" N LEU A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 removed outlier: 3.800A pdb=" N ALA A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 436 removed outlier: 3.665A pdb=" N SER A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 469 removed outlier: 3.973A pdb=" N PHE A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.639A pdb=" N VAL A 489 " --> pdb=" O TRP A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.662A pdb=" N LEU A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 539 removed outlier: 4.246A pdb=" N LYS A 539 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 578 removed outlier: 3.650A pdb=" N ILE A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 610 through 621 removed outlier: 3.845A pdb=" N THR A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU A 617 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 620 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET A 621 " --> pdb=" O GLU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 626 removed outlier: 3.542A pdb=" N LYS A 625 " --> pdb=" O ASN A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.868A pdb=" N ILE A 639 " --> pdb=" O PRO A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.824A pdb=" N ALA A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 704 removed outlier: 4.096A pdb=" N ILE A 700 " --> pdb=" O ASP A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 709 removed outlier: 3.733A pdb=" N ALA A 708 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 709 " --> pdb=" O LYS A 706 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 705 through 709' Processing helix chain 'A' and resid 755 through 760 Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.983A pdb=" N THR A 764 " --> pdb=" O ALA A 761 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 765 " --> pdb=" O MET A 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 765' Processing helix chain 'A' and resid 770 through 779 removed outlier: 3.815A pdb=" N LEU A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA A 779 " --> pdb=" O ARG A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 removed outlier: 4.141A pdb=" N ARG A 788 " --> pdb=" O LYS A 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 228 removed outlier: 3.822A pdb=" N GLU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 260 through 271 removed outlier: 3.674A pdb=" N ALA B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG B 266 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.529A pdb=" N ALA B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 304 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 322 through 326 removed outlier: 4.026A pdb=" N THR B 326 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.504A pdb=" N ARG B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.602A pdb=" N LEU B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG B 368 " --> pdb=" O PRO B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 368' Processing helix chain 'B' and resid 383 through 393 removed outlier: 3.655A pdb=" N ILE B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 413 Processing helix chain 'B' and resid 419 through 436 removed outlier: 3.613A pdb=" N SER B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS B 425 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 469 removed outlier: 3.580A pdb=" N PHE B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 removed outlier: 3.579A pdb=" N LEU B 499 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 500' Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 510 through 517 removed outlier: 3.687A pdb=" N THR B 514 " --> pdb=" O PRO B 510 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 516 " --> pdb=" O GLN B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 579 removed outlier: 3.851A pdb=" N ASP B 571 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 572 " --> pdb=" O ASN B 568 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS B 575 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG B 577 " --> pdb=" O PHE B 573 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 578 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 592 removed outlier: 3.904A pdb=" N ILE B 592 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 620 removed outlier: 3.544A pdb=" N GLU B 617 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N MET B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY B 620 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 639 removed outlier: 3.990A pdb=" N ILE B 639 " --> pdb=" O PRO B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 645 Processing helix chain 'B' and resid 659 through 668 removed outlier: 3.959A pdb=" N LEU B 664 " --> pdb=" O GLU B 660 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 687 Processing helix chain 'B' and resid 693 through 713 removed outlier: 3.790A pdb=" N ARG B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR B 707 " --> pdb=" O ARG B 703 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 709 " --> pdb=" O ALA B 705 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 removed outlier: 4.133A pdb=" N ILE C 216 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 227 Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 236 through 240 removed outlier: 3.902A pdb=" N LEU C 239 " --> pdb=" O HIS C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 271 Processing helix chain 'C' and resid 290 through 305 removed outlier: 3.656A pdb=" N SER C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 344 removed outlier: 3.719A pdb=" N SER C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 395 Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.728A pdb=" N ALA C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA C 411 " --> pdb=" O GLU C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 411' Processing helix chain 'C' and resid 418 through 433 removed outlier: 3.537A pdb=" N SER C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 468 removed outlier: 3.930A pdb=" N PHE C 462 " --> pdb=" O THR C 458 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 467 " --> pdb=" O ARG C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 489 removed outlier: 3.879A pdb=" N ASP C 488 " --> pdb=" O THR C 485 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL C 489 " --> pdb=" O TRP C 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 485 through 489' Processing helix chain 'C' and resid 492 through 499 Processing helix chain 'C' and resid 500 through 502 No H-bonds generated for 'chain 'C' and resid 500 through 502' Processing helix chain 'C' and resid 510 through 517 removed outlier: 3.925A pdb=" N THR C 514 " --> pdb=" O PRO C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 545 removed outlier: 3.749A pdb=" N VAL C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ALA C 542 " --> pdb=" O ALA C 538 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 543 " --> pdb=" O LYS C 539 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL C 545 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 558 removed outlier: 3.669A pdb=" N LEU C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 558 " --> pdb=" O GLY C 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 553 through 558' Processing helix chain 'C' and resid 562 through 566 removed outlier: 4.238A pdb=" N GLU C 566 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 579 removed outlier: 3.720A pdb=" N ILE C 572 " --> pdb=" O ASN C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 592 removed outlier: 3.540A pdb=" N SER C 591 " --> pdb=" O GLN C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 618 removed outlier: 4.241A pdb=" N LEU C 614 " --> pdb=" O VAL C 610 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR C 616 " --> pdb=" O ASN C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 626 removed outlier: 3.759A pdb=" N LYS C 625 " --> pdb=" O ASN C 622 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN C 626 " --> pdb=" O ALA C 623 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 622 through 626' Processing helix chain 'C' and resid 663 through 672 removed outlier: 4.265A pdb=" N LEU C 667 " --> pdb=" O ARG C 663 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 687 removed outlier: 4.252A pdb=" N ILE C 685 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA C 686 " --> pdb=" O LEU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 704 removed outlier: 3.600A pdb=" N VAL C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 216 removed outlier: 3.927A pdb=" N ASP D 215 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE D 216 " --> pdb=" O TYR D 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 212 through 216' Processing helix chain 'D' and resid 219 through 228 removed outlier: 3.816A pdb=" N GLN D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 238 through 244 Processing helix chain 'D' and resid 260 through 271 removed outlier: 3.922A pdb=" N ALA D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 266 " --> pdb=" O THR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.584A pdb=" N VAL D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET D 285 " --> pdb=" O GLY D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 285' Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 315 through 320 removed outlier: 3.808A pdb=" N ILE D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 343 Processing helix chain 'D' and resid 383 through 394 Processing helix chain 'D' and resid 406 through 412 Processing helix chain 'D' and resid 417 through 435 removed outlier: 3.889A pdb=" N ILE D 421 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA D 422 " --> pdb=" O GLY D 418 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 492 through 501 removed outlier: 3.695A pdb=" N GLU D 497 " --> pdb=" O ASP D 493 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.600A pdb=" N VAL D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 542 " --> pdb=" O ALA D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 579 Processing helix chain 'D' and resid 609 through 618 removed outlier: 3.846A pdb=" N THR D 616 " --> pdb=" O ASN D 612 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 671 removed outlier: 3.844A pdb=" N SER D 665 " --> pdb=" O ASN D 661 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA D 669 " --> pdb=" O SER D 665 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 689 Processing helix chain 'D' and resid 693 through 714 removed outlier: 3.601A pdb=" N ILE D 700 " --> pdb=" O ASP D 696 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 236 removed outlier: 4.156A pdb=" N ILE E 226 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N MET E 229 " --> pdb=" O GLN E 225 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL E 230 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Proline residue: E 233 - end of helix removed outlier: 3.826A pdb=" N HIS E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 273 removed outlier: 3.767A pdb=" N ARG E 266 " --> pdb=" O THR E 262 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 285 removed outlier: 3.504A pdb=" N MET E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 305 removed outlier: 3.868A pdb=" N LYS E 305 " --> pdb=" O GLU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 319 Processing helix chain 'E' and resid 331 through 342 removed outlier: 3.737A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN E 337 " --> pdb=" O ARG E 333 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 339 " --> pdb=" O VAL E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 387 through 397 removed outlier: 3.537A pdb=" N LYS E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN E 397 " --> pdb=" O ILE E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 removed outlier: 4.089A pdb=" N LEU E 409 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 437 removed outlier: 3.779A pdb=" N CYS E 425 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN E 431 " --> pdb=" O GLU E 427 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS E 436 " --> pdb=" O GLN E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 456 removed outlier: 3.842A pdb=" N GLY E 456 " --> pdb=" O ASP E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 468 removed outlier: 3.606A pdb=" N PHE E 462 " --> pdb=" O THR E 458 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG E 463 " --> pdb=" O MET E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 499 removed outlier: 3.542A pdb=" N GLU E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 509 Processing helix chain 'E' and resid 511 through 517 removed outlier: 3.517A pdb=" N LYS E 515 " --> pdb=" O ASP E 511 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE E 516 " --> pdb=" O GLN E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 543 removed outlier: 3.706A pdb=" N ALA E 542 " --> pdb=" O ALA E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 579 removed outlier: 3.761A pdb=" N ARG E 577 " --> pdb=" O PHE E 573 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA E 579 " --> pdb=" O LYS E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 592 removed outlier: 3.512A pdb=" N ILE E 592 " --> pdb=" O LEU E 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 589 through 592' Processing helix chain 'E' and resid 601 through 621 removed outlier: 3.672A pdb=" N ARG E 609 " --> pdb=" O GLY E 605 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL E 610 " --> pdb=" O ALA E 606 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN E 612 " --> pdb=" O ASP E 608 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLN E 613 " --> pdb=" O ARG E 609 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU E 614 " --> pdb=" O VAL E 610 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP E 619 " --> pdb=" O LEU E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 663 through 669 removed outlier: 3.654A pdb=" N ILE E 666 " --> pdb=" O ARG E 663 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 667 " --> pdb=" O LEU E 664 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN E 668 " --> pdb=" O SER E 665 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA E 669 " --> pdb=" O ILE E 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 663 through 669' Processing helix chain 'E' and resid 681 through 687 Processing helix chain 'E' and resid 703 through 708 Processing helix chain 'E' and resid 709 through 713 removed outlier: 3.734A pdb=" N SER E 712 " --> pdb=" O ILE E 709 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE E 713 " --> pdb=" O LYS E 710 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 709 through 713' Processing helix chain 'F' and resid 222 through 230 removed outlier: 3.913A pdb=" N GLU F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL F 230 " --> pdb=" O ILE F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 236 removed outlier: 4.027A pdb=" N HIS F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 removed outlier: 4.089A pdb=" N VAL F 268 " --> pdb=" O MET F 264 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA F 269 " --> pdb=" O ALA F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 288 through 301 removed outlier: 3.514A pdb=" N GLU F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 297 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 332 through 343 removed outlier: 4.341A pdb=" N LEU F 338 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 339 " --> pdb=" O VAL F 335 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 363 removed outlier: 3.525A pdb=" N SER F 362 " --> pdb=" O ARG F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 395 Processing helix chain 'F' and resid 407 through 413 removed outlier: 3.506A pdb=" N THR F 413 " --> pdb=" O LEU F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 435 removed outlier: 3.630A pdb=" N SER F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU F 435 " --> pdb=" O GLN F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 467 removed outlier: 4.133A pdb=" N PHE F 462 " --> pdb=" O THR F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 489 removed outlier: 3.695A pdb=" N VAL F 489 " --> pdb=" O TRP F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 501 removed outlier: 3.614A pdb=" N LYS F 496 " --> pdb=" O LEU F 492 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU F 497 " --> pdb=" O ASP F 493 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU F 498 " --> pdb=" O GLU F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 515 removed outlier: 3.739A pdb=" N THR F 514 " --> pdb=" O PRO F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 540 removed outlier: 3.636A pdb=" N LEU F 537 " --> pdb=" O GLY F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 545 removed outlier: 4.321A pdb=" N GLU F 544 " --> pdb=" O ALA F 540 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL F 545 " --> pdb=" O VAL F 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 540 through 545' Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 567 through 572 removed outlier: 3.663A pdb=" N ILE F 572 " --> pdb=" O ASN F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 579 Processing helix chain 'F' and resid 610 through 618 removed outlier: 4.379A pdb=" N LEU F 615 " --> pdb=" O VAL F 611 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N THR F 616 " --> pdb=" O ASN F 612 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET F 618 " --> pdb=" O LEU F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 659 through 671 removed outlier: 3.502A pdb=" N LEU F 664 " --> pdb=" O GLU F 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 682 through 687 removed outlier: 3.765A pdb=" N ALA F 686 " --> pdb=" O LEU F 682 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS F 687 " --> pdb=" O THR F 683 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 682 through 687' Processing helix chain 'F' and resid 699 through 704 Processing helix chain 'F' and resid 705 through 707 No H-bonds generated for 'chain 'F' and resid 705 through 707' Processing helix chain 'F' and resid 709 through 714 removed outlier: 3.593A pdb=" N ILE F 713 " --> pdb=" O ILE F 709 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 31 removed outlier: 3.502A pdb=" N VAL K 26 " --> pdb=" O THR K 22 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER K 28 " --> pdb=" O ASP K 24 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN K 31 " --> pdb=" O LYS K 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 135 removed outlier: 3.830A pdb=" N VAL H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS H 133 " --> pdb=" O LYS H 129 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 234 Processing helix chain 'J' and resid 255 through 260 removed outlier: 4.442A pdb=" N TYR J 259 " --> pdb=" O THR J 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 125 removed outlier: 3.729A pdb=" N GLU G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU G 125 " --> pdb=" O GLU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 162 removed outlier: 3.645A pdb=" N HIS G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN G 162 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 181 removed outlier: 3.627A pdb=" N TYR G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN G 179 " --> pdb=" O LYS G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 256 removed outlier: 3.729A pdb=" N GLU G 247 " --> pdb=" O GLU G 243 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE G 248 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TRP G 252 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 318 removed outlier: 3.732A pdb=" N VAL G 303 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN G 309 " --> pdb=" O ASN G 305 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE G 310 " --> pdb=" O GLU G 306 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG G 312 " --> pdb=" O LEU G 308 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN G 315 " --> pdb=" O ASP G 311 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU G 316 " --> pdb=" O ARG G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 365 removed outlier: 3.762A pdb=" N ILE G 356 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET G 357 " --> pdb=" O LEU G 353 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS G 361 " --> pdb=" O MET G 357 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS G 365 " --> pdb=" O HIS G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 3.572A pdb=" N VAL G 409 " --> pdb=" O ALA G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 501 through 508 removed outlier: 3.647A pdb=" N LYS G 505 " --> pdb=" O TYR G 501 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS G 506 " --> pdb=" O GLN G 502 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU G 508 " --> pdb=" O LEU G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 516 through 525 removed outlier: 4.201A pdb=" N GLU G 522 " --> pdb=" O ASN G 518 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS G 523 " --> pdb=" O LEU G 519 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE G 524 " --> pdb=" O LEU G 520 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER G 525 " --> pdb=" O HIS G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 537 removed outlier: 3.608A pdb=" N ASN G 534 " --> pdb=" O LEU G 530 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER G 535 " --> pdb=" O LEU G 531 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU G 536 " --> pdb=" O TYR G 532 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN G 537 " --> pdb=" O ILE G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 553 Processing helix chain 'G' and resid 556 through 566 removed outlier: 3.736A pdb=" N LEU G 561 " --> pdb=" O GLU G 557 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS G 562 " --> pdb=" O GLU G 558 " (cutoff:3.500A) Processing helix chain 'G' and resid 566 through 579 removed outlier: 3.621A pdb=" N GLN G 570 " --> pdb=" O SER G 566 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU G 578 " --> pdb=" O MET G 574 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER G 579 " --> pdb=" O ILE G 575 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 279 removed outlier: 6.300A pdb=" N PHE A 275 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 312 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE A 277 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 356 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLY A 250 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 377 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU A 252 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 549 through 552 removed outlier: 3.563A pdb=" N ILE A 550 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE A 585 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 587 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL A 524 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY A 523 " --> pdb=" O GLN A 651 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE A 653 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU A 525 " --> pdb=" O ILE A 653 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 277 through 279 removed outlier: 6.222A pdb=" N LEU B 252 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 523 through 526 removed outlier: 3.694A pdb=" N VAL B 524 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE B 628 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 275 through 276 removed outlier: 6.053A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA C 309 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE C 354 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE C 311 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ALA C 356 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE C 313 " --> pdb=" O ALA C 356 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL C 377 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU C 252 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 629 through 630 removed outlier: 3.648A pdb=" N GLN C 651 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR C 527 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 548 through 549 removed outlier: 6.426A pdb=" N ASN C 548 " --> pdb=" O VAL C 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 375 through 378 removed outlier: 3.739A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET G 144 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 278 " --> pdb=" O MET G 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 548 through 551 removed outlier: 5.454A pdb=" N THR D 582 " --> pdb=" O PHE D 628 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE D 630 " --> pdb=" O THR D 582 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL D 584 " --> pdb=" O ILE D 630 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA D 632 " --> pdb=" O VAL D 584 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU D 586 " --> pdb=" O ALA D 632 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN D 651 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR D 527 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 275 through 276 removed outlier: 6.551A pdb=" N PHE E 275 " --> pdb=" O ILE E 310 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE E 312 " --> pdb=" O PHE E 275 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL E 352 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E 311 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR E 254 " --> pdb=" O VAL E 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 548 through 553 removed outlier: 6.148A pdb=" N ASN E 548 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N PHE E 585 " --> pdb=" O ASN E 548 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE E 550 " --> pdb=" O PHE E 585 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASP E 587 " --> pdb=" O ILE E 550 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL E 552 " --> pdb=" O ASP E 587 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ILE E 630 " --> pdb=" O THR E 582 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL E 584 " --> pdb=" O ILE E 630 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ALA E 632 " --> pdb=" O VAL E 584 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU E 586 " --> pdb=" O ALA E 632 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL E 524 " --> pdb=" O GLY E 631 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU E 525 " --> pdb=" O ILE E 653 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 275 through 280 removed outlier: 5.771A pdb=" N PHE F 275 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE F 312 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE F 277 " --> pdb=" O PHE F 312 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ASP F 314 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE F 279 " --> pdb=" O ASP F 314 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL F 352 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F 311 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL F 251 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR F 357 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N MET F 253 " --> pdb=" O THR F 357 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU F 252 " --> pdb=" O VAL F 377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 523 through 527 removed outlier: 7.137A pdb=" N GLY F 523 " --> pdb=" O LEU F 649 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN F 651 " --> pdb=" O GLY F 523 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 550 through 551 removed outlier: 7.249A pdb=" N THR F 582 " --> pdb=" O PHE F 628 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ILE F 630 " --> pdb=" O THR F 582 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL F 584 " --> pdb=" O ILE F 630 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 112 through 116 removed outlier: 3.605A pdb=" N LEU H 115 " --> pdb=" O ILE H 103 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N LEU H 167 " --> pdb=" O GLN H 102 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE H 104 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU H 169 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS H 106 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LEU H 171 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 212 through 216 removed outlier: 3.672A pdb=" N LEU J 215 " --> pdb=" O ILE J 203 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE J 203 " --> pdb=" O LEU J 215 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLN J 202 " --> pdb=" O SER J 265 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N LEU J 267 " --> pdb=" O GLN J 202 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE J 204 " --> pdb=" O LEU J 267 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU J 269 " --> pdb=" O PHE J 204 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS J 206 " --> pdb=" O LEU J 269 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS J 268 " --> pdb=" O ILE J 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 236 through 238 removed outlier: 3.932A pdb=" N HIS G 236 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL G 281 " --> pdb=" O GLU G 238 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE G 277 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR G 270 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ALA G 279 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER G 268 " --> pdb=" O ALA G 279 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL G 281 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER G 266 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY G 261 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU G 324 " --> pdb=" O GLY G 261 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET G 263 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N VAL G 382 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE G 322 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N CYS G 384 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU G 324 " --> pdb=" O CYS G 384 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE G 386 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE G 326 " --> pdb=" O ILE G 386 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR G 383 " --> pdb=" O TYR G 399 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 422 through 423 720 hydrogen bonds defined for protein. 2058 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: 8.16 Time building geometry restraints manager: 12.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5059 1.31 - 1.44: 6993 1.44 - 1.57: 17161 1.57 - 1.69: 48 1.69 - 1.82: 238 Bond restraints: 29499 Sorted by residual: bond pdb=" C4 ATP D 902 " pdb=" C5 ATP D 902 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.02e+01 bond pdb=" C4 ATP C1003 " pdb=" C5 ATP C1003 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.99e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.97e+01 bond pdb=" C4 ATP C1002 " pdb=" C5 ATP C1002 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP B 901 " pdb=" C5 ATP B 901 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.89e+01 ... (remaining 29494 not shown) Histogram of bond angle deviations from ideal: 70.76 - 83.84: 1 83.84 - 96.92: 1 96.92 - 109.99: 4251 109.99 - 123.07: 34102 123.07 - 136.15: 1578 Bond angle restraints: 39933 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP C1002 " pdb=" O3B ATP C1002 " pdb=" PG ATP C1002 " ideal model delta sigma weight residual 139.87 120.47 19.40 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PB ATP C1003 " pdb=" O3B ATP C1003 " pdb=" PG ATP C1003 " ideal model delta sigma weight residual 139.87 120.47 19.40 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 120.49 19.38 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB ATP C1001 " pdb=" O3B ATP C1001 " pdb=" PG ATP C1001 " ideal model delta sigma weight residual 139.87 120.50 19.37 1.00e+00 1.00e+00 3.75e+02 ... (remaining 39928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.26: 17561 30.26 - 60.51: 634 60.51 - 90.77: 86 90.77 - 121.03: 0 121.03 - 151.29: 3 Dihedral angle restraints: 18284 sinusoidal: 7626 harmonic: 10658 Sorted by residual: dihedral pdb=" C LEU K 43 " pdb=" N LEU K 43 " pdb=" CA LEU K 43 " pdb=" CB LEU K 43 " ideal model delta harmonic sigma weight residual -122.60 -141.64 19.04 0 2.50e+00 1.60e-01 5.80e+01 dihedral pdb=" CA ASN G 510 " pdb=" C ASN G 510 " pdb=" N VAL G 511 " pdb=" CA VAL G 511 " ideal model delta harmonic sigma weight residual -180.00 -145.37 -34.63 0 5.00e+00 4.00e-02 4.80e+01 dihedral pdb=" N LEU K 43 " pdb=" C LEU K 43 " pdb=" CA LEU K 43 " pdb=" CB LEU K 43 " ideal model delta harmonic sigma weight residual 122.80 139.88 -17.08 0 2.50e+00 1.60e-01 4.67e+01 ... (remaining 18281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.196: 4475 0.196 - 0.391: 8 0.391 - 0.587: 1 0.587 - 0.782: 0 0.782 - 0.978: 1 Chirality restraints: 4485 Sorted by residual: chirality pdb=" CA LEU K 43 " pdb=" N LEU K 43 " pdb=" C LEU K 43 " pdb=" CB LEU K 43 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CG LEU K 43 " pdb=" CB LEU K 43 " pdb=" CD1 LEU K 43 " pdb=" CD2 LEU K 43 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CA ARG K 42 " pdb=" N ARG K 42 " pdb=" C ARG K 42 " pdb=" CB ARG K 42 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 4482 not shown) Planarity restraints: 5212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE K 36 " 0.168 5.00e-02 4.00e+02 2.67e-01 1.14e+02 pdb=" N PRO K 37 " -0.458 5.00e-02 4.00e+02 pdb=" CA PRO K 37 " 0.194 5.00e-02 4.00e+02 pdb=" CD PRO K 37 " 0.096 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 37 " -0.135 5.00e-02 4.00e+02 2.15e-01 7.39e+01 pdb=" N PRO K 38 " 0.371 5.00e-02 4.00e+02 pdb=" CA PRO K 38 " -0.143 5.00e-02 4.00e+02 pdb=" CD PRO K 38 " -0.092 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN K 41 " -0.014 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLN K 41 " 0.055 2.00e-02 2.50e+03 pdb=" O GLN K 41 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG K 42 " -0.019 2.00e-02 2.50e+03 ... (remaining 5209 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.25: 27 2.25 - 2.91: 11389 2.91 - 3.57: 39352 3.57 - 4.24: 66063 4.24 - 4.90: 105566 Nonbonded interactions: 222397 Sorted by model distance: nonbonded pdb=" O GLY B 531 " pdb=" O5' ATP C1001 " model vdw 1.585 3.040 nonbonded pdb=" NH1 ARG C 645 " pdb=" O1B ATP C1001 " model vdw 1.654 2.496 nonbonded pdb=" OG SER D 559 " pdb=" CE1 TYR E 562 " model vdw 1.865 3.340 nonbonded pdb=" O THR B 532 " pdb=" O2B ATP C1001 " model vdw 1.913 3.040 nonbonded pdb=" CE1 TYR D 562 " pdb=" NH2 ARG D 609 " model vdw 1.917 3.420 ... (remaining 222392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 209 through 437 or resid 459 through 713 or resid 901)) selection = (chain 'B' and (resid 209 through 437 or resid 459 through 713 or resid 901)) selection = (chain 'C' and (resid 209 through 437 or resid 459 through 713 or resid 1003)) selection = (chain 'D' and (resid 209 through 713 or resid 902)) selection = (chain 'E' and (resid 209 through 437 or resid 459 through 713 or resid 902)) selection = (chain 'F' and (resid 209 through 437 or resid 459 through 713 or resid 901)) } ncs_group { reference = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.050 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 74.590 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 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 : 0.004 0.084 29499 Z= 0.274 Angle : 0.991 54.241 39933 Z= 0.642 Chirality : 0.051 0.978 4485 Planarity : 0.007 0.267 5212 Dihedral : 15.455 151.287 11414 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.54 % Favored : 93.24 % Rotamer: Outliers : 0.45 % Allowed : 7.74 % Favored : 91.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.28 (0.10), residues: 3684 helix: -4.93 (0.04), residues: 1291 sheet: -1.97 (0.23), residues: 411 loop : -2.84 (0.11), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 211 HIS 0.004 0.001 HIS G 208 PHE 0.014 0.001 PHE G 340 TYR 0.009 0.001 TYR E 562 ARG 0.005 0.000 ARG K 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 805 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ILE cc_start: 0.8309 (tp) cc_final: 0.8085 (tp) REVERT: A 310 ILE cc_start: 0.8598 (mt) cc_final: 0.8346 (tt) REVERT: A 332 ARG cc_start: 0.7717 (ptt180) cc_final: 0.7348 (ptt-90) REVERT: A 350 ASN cc_start: 0.7778 (p0) cc_final: 0.7508 (p0) REVERT: A 459 MET cc_start: 0.8290 (ptm) cc_final: 0.8044 (ttp) REVERT: A 526 PHE cc_start: 0.9379 (m-80) cc_final: 0.9044 (m-80) REVERT: A 624 LYS cc_start: 0.5577 (tttm) cc_final: 0.4282 (mmtm) REVERT: A 628 PHE cc_start: 0.7926 (m-80) cc_final: 0.7557 (m-80) REVERT: A 784 MET cc_start: 0.1607 (tpp) cc_final: 0.0475 (tpt) REVERT: B 264 MET cc_start: 0.8429 (ttp) cc_final: 0.8096 (ttp) REVERT: B 283 GLU cc_start: 0.7900 (tt0) cc_final: 0.7690 (mt-10) REVERT: B 285 MET cc_start: 0.7218 (tmm) cc_final: 0.6921 (tmm) REVERT: B 301 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 302 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8105 (tp30) REVERT: B 326 THR cc_start: 0.5099 (t) cc_final: 0.4523 (m) REVERT: B 331 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8649 (tp30) REVERT: B 420 ASP cc_start: 0.8267 (m-30) cc_final: 0.7982 (m-30) REVERT: B 427 GLU cc_start: 0.8380 (tt0) cc_final: 0.8162 (tp30) REVERT: B 477 THR cc_start: 0.6773 (t) cc_final: 0.6319 (m) REVERT: B 496 LYS cc_start: 0.8573 (mtmt) cc_final: 0.8279 (mtpt) REVERT: B 560 MET cc_start: 0.4964 (ttt) cc_final: 0.4743 (tpt) REVERT: B 614 LEU cc_start: 0.8863 (mt) cc_final: 0.8245 (pp) REVERT: C 229 MET cc_start: 0.7513 (mtm) cc_final: 0.7111 (tmm) REVERT: C 236 HIS cc_start: 0.5433 (t-170) cc_final: 0.5077 (t-170) REVERT: C 264 MET cc_start: 0.8751 (tpt) cc_final: 0.8447 (tpp) REVERT: C 304 GLU cc_start: 0.8161 (tt0) cc_final: 0.7895 (tt0) REVERT: C 324 ASP cc_start: 0.8450 (p0) cc_final: 0.7964 (t0) REVERT: C 430 MET cc_start: 0.8482 (mmt) cc_final: 0.8243 (mmm) REVERT: C 474 LEU cc_start: 0.6597 (mt) cc_final: 0.6170 (tt) REVERT: C 513 TYR cc_start: 0.8239 (m-80) cc_final: 0.7481 (m-80) REVERT: C 518 LEU cc_start: 0.7976 (tp) cc_final: 0.7684 (mt) REVERT: C 574 ASP cc_start: 0.8602 (t0) cc_final: 0.8083 (t0) REVERT: C 621 MET cc_start: 0.6050 (mmm) cc_final: 0.5818 (mmm) REVERT: D 251 VAL cc_start: 0.9011 (p) cc_final: 0.8801 (p) REVERT: D 302 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7836 (mm-30) REVERT: D 513 TYR cc_start: 0.6819 (m-80) cc_final: 0.6364 (m-10) REVERT: D 621 MET cc_start: 0.8453 (ppp) cc_final: 0.8049 (ppp) REVERT: D 698 LEU cc_start: 0.7778 (mt) cc_final: 0.7416 (mt) REVERT: E 278 LEU cc_start: 0.8516 (mt) cc_final: 0.8309 (mt) REVERT: E 342 MET cc_start: 0.8382 (mmm) cc_final: 0.8108 (ttm) REVERT: E 345 MET cc_start: 0.7484 (ptp) cc_final: 0.6898 (ptt) REVERT: E 513 TYR cc_start: 0.7861 (p90) cc_final: 0.7491 (p90) REVERT: E 636 PRO cc_start: 0.6351 (Cg_endo) cc_final: 0.6109 (Cg_exo) REVERT: F 264 MET cc_start: 0.9032 (ptp) cc_final: 0.8678 (ptm) REVERT: F 285 MET cc_start: 0.8809 (tpp) cc_final: 0.7523 (tpp) REVERT: F 291 GLU cc_start: 0.8676 (tp30) cc_final: 0.8289 (tp30) REVERT: F 324 ASP cc_start: 0.9069 (m-30) cc_final: 0.8472 (p0) REVERT: F 367 LEU cc_start: 0.8869 (mp) cc_final: 0.8653 (mp) REVERT: F 398 MET cc_start: 0.8701 (mmm) cc_final: 0.8474 (mmm) REVERT: F 504 GLU cc_start: 0.7610 (pp20) cc_final: 0.6980 (mp0) REVERT: F 618 MET cc_start: 0.6638 (ttm) cc_final: 0.6217 (ttm) REVERT: K 6 LYS cc_start: 0.5018 (mmmm) cc_final: 0.4712 (mmmt) REVERT: K 15 LEU cc_start: 0.7748 (mm) cc_final: 0.7497 (mm) REVERT: H 118 GLU cc_start: 0.9230 (mp0) cc_final: 0.8972 (mp0) REVERT: H 123 ILE cc_start: 0.8333 (mm) cc_final: 0.8118 (mm) REVERT: H 141 GLN cc_start: 0.7119 (mt0) cc_final: 0.6037 (mt0) REVERT: J 201 MET cc_start: 0.8342 (ptt) cc_final: 0.7846 (ppp) REVERT: J 221 ASP cc_start: 0.6974 (t0) cc_final: 0.6260 (t0) REVERT: J 250 LEU cc_start: 0.6903 (mt) cc_final: 0.6291 (tt) REVERT: G 121 GLU cc_start: 0.8342 (tt0) cc_final: 0.8026 (tp30) REVERT: G 161 LYS cc_start: 0.8447 (tmtt) cc_final: 0.8149 (ttmt) REVERT: G 191 SER cc_start: 0.7502 (t) cc_final: 0.6928 (p) REVERT: G 257 MET cc_start: 0.8585 (mmt) cc_final: 0.8284 (mmm) REVERT: G 370 LYS cc_start: 0.7917 (ttmt) cc_final: 0.7006 (tptt) REVERT: G 406 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7978 (tm-30) REVERT: G 424 TYR cc_start: 0.6078 (t80) cc_final: 0.5612 (t80) REVERT: G 429 THR cc_start: 0.7752 (p) cc_final: 0.7536 (t) REVERT: G 430 ASP cc_start: 0.7764 (t0) cc_final: 0.6900 (t0) REVERT: G 485 THR cc_start: 0.5559 (p) cc_final: 0.5214 (m) REVERT: G 539 LEU cc_start: 0.7750 (mt) cc_final: 0.7530 (tp) outliers start: 14 outliers final: 5 residues processed: 815 average time/residue: 0.4499 time to fit residues: 556.0752 Evaluate side-chains 461 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 456 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 562 TYR Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 562 TYR Chi-restraints excluded: chain K residue 44 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 20.0000 chunk 277 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 148 optimal weight: 0.7980 chunk 286 optimal weight: 40.0000 chunk 111 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 chunk 332 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 GLN A 757 HIS B 238 GLN B 432 GLN B 626 ASN C 238 GLN C 270 ASN C 337 GLN C 394 HIS ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN D 337 GLN D 468 ASN D 702 GLN ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 ASN E 568 ASN E 612 ASN F 270 ASN F 337 GLN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 468 ASN F 509 HIS F 512 GLN ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN K 2 GLN K 25 ASN K 31 GLN H 125 ASN H 149 GLN H 162 GLN G 162 ASN G 272 ASN G 293 GLN G 305 ASN G 491 ASN G 577 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29499 Z= 0.234 Angle : 0.702 18.361 39933 Z= 0.354 Chirality : 0.045 0.170 4485 Planarity : 0.006 0.171 5212 Dihedral : 12.081 142.400 4332 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.13 % Favored : 93.81 % Rotamer: Outliers : 2.46 % Allowed : 15.54 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.11), residues: 3684 helix: -3.04 (0.10), residues: 1305 sheet: -1.35 (0.25), residues: 375 loop : -2.33 (0.12), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 561 HIS 0.014 0.001 HIS D 414 PHE 0.019 0.002 PHE G 169 TYR 0.018 0.002 TYR E 527 ARG 0.011 0.001 ARG A 672 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 461 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 MET cc_start: 0.8750 (tpp) cc_final: 0.8472 (tpt) REVERT: A 350 ASN cc_start: 0.8204 (p0) cc_final: 0.7945 (p0) REVERT: A 443 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8453 (t0) REVERT: A 459 MET cc_start: 0.8422 (ptm) cc_final: 0.7971 (ttp) REVERT: A 526 PHE cc_start: 0.9391 (m-80) cc_final: 0.9152 (m-80) REVERT: A 621 MET cc_start: 0.8623 (mmp) cc_final: 0.7891 (mmm) REVERT: A 624 LYS cc_start: 0.5201 (tttm) cc_final: 0.4207 (mppt) REVERT: A 784 MET cc_start: 0.1253 (tpp) cc_final: 0.0051 (tpt) REVERT: B 264 MET cc_start: 0.7966 (ttp) cc_final: 0.7591 (ttp) REVERT: B 301 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7619 (tm-30) REVERT: B 302 GLU cc_start: 0.8490 (mm-30) cc_final: 0.7947 (tp30) REVERT: B 427 GLU cc_start: 0.8226 (tt0) cc_final: 0.7815 (tt0) REVERT: B 479 VAL cc_start: 0.6091 (OUTLIER) cc_final: 0.5863 (t) REVERT: B 614 LEU cc_start: 0.8699 (mt) cc_final: 0.8124 (pp) REVERT: B 706 LYS cc_start: 0.9250 (mmtm) cc_final: 0.8966 (pptt) REVERT: C 288 MET cc_start: 0.7299 (tpp) cc_final: 0.6511 (tpp) REVERT: C 324 ASP cc_start: 0.8558 (p0) cc_final: 0.8041 (t0) REVERT: C 339 LEU cc_start: 0.8321 (mt) cc_final: 0.8118 (mt) REVERT: C 430 MET cc_start: 0.8639 (mmt) cc_final: 0.8405 (mmm) REVERT: C 474 LEU cc_start: 0.6529 (mt) cc_final: 0.6227 (tt) REVERT: C 513 TYR cc_start: 0.8420 (m-80) cc_final: 0.7585 (m-80) REVERT: D 302 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7601 (mm-30) REVERT: D 513 TYR cc_start: 0.6700 (m-80) cc_final: 0.6295 (m-80) REVERT: D 621 MET cc_start: 0.8429 (ppp) cc_final: 0.8030 (ppp) REVERT: E 278 LEU cc_start: 0.8391 (mt) cc_final: 0.8175 (mt) REVERT: E 302 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7515 (mt-10) REVERT: E 342 MET cc_start: 0.8797 (mmm) cc_final: 0.8281 (mmm) REVERT: E 345 MET cc_start: 0.7341 (ptp) cc_final: 0.7087 (ptt) REVERT: E 398 MET cc_start: 0.3238 (ttp) cc_final: 0.2143 (tpp) REVERT: E 501 GLU cc_start: 0.8551 (mp0) cc_final: 0.7925 (pm20) REVERT: E 513 TYR cc_start: 0.7602 (p90) cc_final: 0.7248 (p90) REVERT: E 527 TYR cc_start: 0.6674 (p90) cc_final: 0.6424 (p90) REVERT: E 602 ASP cc_start: 0.7506 (t70) cc_final: 0.7279 (t0) REVERT: F 264 MET cc_start: 0.9051 (ptp) cc_final: 0.8295 (ptm) REVERT: F 285 MET cc_start: 0.8722 (tpp) cc_final: 0.8279 (tpp) REVERT: F 286 SER cc_start: 0.6892 (p) cc_final: 0.6471 (m) REVERT: F 291 GLU cc_start: 0.8878 (tp30) cc_final: 0.8575 (tp30) REVERT: F 314 ASP cc_start: 0.8427 (t70) cc_final: 0.7338 (t0) REVERT: F 324 ASP cc_start: 0.9063 (m-30) cc_final: 0.8354 (p0) REVERT: F 342 MET cc_start: 0.8430 (mmm) cc_final: 0.8141 (mmm) REVERT: F 430 MET cc_start: 0.8563 (mmm) cc_final: 0.8315 (mmm) REVERT: F 504 GLU cc_start: 0.7845 (pp20) cc_final: 0.7104 (mp0) REVERT: F 564 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7768 (mp0) REVERT: K 16 GLU cc_start: 0.5718 (mp0) cc_final: 0.5028 (mp0) REVERT: H 163 LYS cc_start: 0.8806 (tppp) cc_final: 0.8206 (mmmm) REVERT: J 201 MET cc_start: 0.8539 (ptt) cc_final: 0.7710 (ppp) REVERT: J 221 ASP cc_start: 0.6471 (t0) cc_final: 0.6263 (t0) REVERT: G 157 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7658 (tm-30) REVERT: G 161 LYS cc_start: 0.8433 (tmtt) cc_final: 0.8211 (ttmt) REVERT: G 191 SER cc_start: 0.7730 (t) cc_final: 0.7440 (p) REVERT: G 233 MET cc_start: 0.8990 (mmm) cc_final: 0.8781 (mmm) REVERT: G 257 MET cc_start: 0.8487 (mmt) cc_final: 0.8169 (mmm) REVERT: G 370 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7087 (tptt) REVERT: G 422 MET cc_start: 0.7668 (mtt) cc_final: 0.7427 (mtp) REVERT: G 427 ASP cc_start: 0.7730 (t0) cc_final: 0.7211 (t0) REVERT: G 430 ASP cc_start: 0.8204 (t0) cc_final: 0.7622 (t0) REVERT: G 574 MET cc_start: 0.8645 (tpt) cc_final: 0.8329 (tpp) outliers start: 76 outliers final: 44 residues processed: 513 average time/residue: 0.3923 time to fit residues: 321.8538 Evaluate side-chains 419 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 373 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 526 PHE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 693 SER Chi-restraints excluded: chain E residue 515 LYS Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 512 GLN Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain J residue 233 LYS Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 544 TRP Chi-restraints excluded: chain G residue 546 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 276 optimal weight: 7.9990 chunk 226 optimal weight: 20.0000 chunk 91 optimal weight: 0.0980 chunk 332 optimal weight: 3.9990 chunk 359 optimal weight: 0.0980 chunk 296 optimal weight: 20.0000 chunk 330 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 267 optimal weight: 10.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 GLN ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 668 ASN ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 GLN ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 509 HIS ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN K 25 ASN J 249 GLN G 305 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3604 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: