Starting phenix.real_space_refine (version: dev) on Mon Feb 27 22:18:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rli_24531/02_2023/7rli_24531_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rli_24531/02_2023/7rli_24531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rli_24531/02_2023/7rli_24531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rli_24531/02_2023/7rli_24531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rli_24531/02_2023/7rli_24531_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rli_24531/02_2023/7rli_24531_updated.pdb" } resolution = 3.1 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= -0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 372 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B ASP 307": "OD1" <-> "OD2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C ASP 307": "OD1" <-> "OD2" Residue "C ASP 478": "OD1" <-> "OD2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "D TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D ASP 307": "OD1" <-> "OD2" Residue "D ASP 478": "OD1" <-> "OD2" Residue "D GLU 488": "OE1" <-> "OE2" Residue "D ASP 627": "OD1" <-> "OD2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "E TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E ASP 307": "OD1" <-> "OD2" Residue "E ASP 478": "OD1" <-> "OD2" Residue "E GLU 488": "OE1" <-> "OE2" Residue "E ASP 627": "OD1" <-> "OD2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "E GLU 701": "OE1" <-> "OE2" Residue "F TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F ASP 307": "OD1" <-> "OD2" Residue "F ASP 478": "OD1" <-> "OD2" Residue "F GLU 488": "OE1" <-> "OE2" Residue "F ASP 627": "OD1" <-> "OD2" Residue "F GLU 689": "OE1" <-> "OE2" Residue "F GLU 701": "OE1" <-> "OE2" Residue "G TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G ASP 307": "OD1" <-> "OD2" Residue "G ASP 478": "OD1" <-> "OD2" Residue "G GLU 488": "OE1" <-> "OE2" Residue "G ASP 627": "OD1" <-> "OD2" Residue "G GLU 689": "OE1" <-> "OE2" Residue "G GLU 701": "OE1" <-> "OE2" Residue "H TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "H ASP 307": "OD1" <-> "OD2" Residue "H ASP 478": "OD1" <-> "OD2" Residue "H GLU 488": "OE1" <-> "OE2" Residue "H ASP 627": "OD1" <-> "OD2" Residue "H GLU 689": "OE1" <-> "OE2" Residue "H GLU 701": "OE1" <-> "OE2" Residue "I TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I ASP 307": "OD1" <-> "OD2" Residue "I ASP 478": "OD1" <-> "OD2" Residue "I GLU 488": "OE1" <-> "OE2" Residue "I ASP 627": "OD1" <-> "OD2" Residue "I GLU 689": "OE1" <-> "OE2" Residue "I GLU 701": "OE1" <-> "OE2" Residue "J TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 218": "OE1" <-> "OE2" Residue "J ASP 307": "OD1" <-> "OD2" Residue "J ASP 478": "OD1" <-> "OD2" Residue "J GLU 488": "OE1" <-> "OE2" Residue "J ASP 627": "OD1" <-> "OD2" Residue "J GLU 689": "OE1" <-> "OE2" Residue "J GLU 701": "OE1" <-> "OE2" Residue "K TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 218": "OE1" <-> "OE2" Residue "K ASP 307": "OD1" <-> "OD2" Residue "K ASP 478": "OD1" <-> "OD2" Residue "K GLU 488": "OE1" <-> "OE2" Residue "K ASP 627": "OD1" <-> "OD2" Residue "K GLU 689": "OE1" <-> "OE2" Residue "K GLU 701": "OE1" <-> "OE2" Residue "L TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 218": "OE1" <-> "OE2" Residue "L ASP 307": "OD1" <-> "OD2" Residue "L ASP 478": "OD1" <-> "OD2" Residue "L GLU 488": "OE1" <-> "OE2" Residue "L ASP 627": "OD1" <-> "OD2" Residue "L GLU 689": "OE1" <-> "OE2" Residue "L GLU 701": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 69768 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "B" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "C" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "D" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "E" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "F" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "G" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "H" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "I" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "J" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "K" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "L" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} 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, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 28.46, per 1000 atoms: 0.41 Number of scatterers: 69768 At special positions: 0 Unit cell: (173, 177, 185, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 360 16.00 P 24 15.00 O 13200 8.00 N 12300 7.00 C 43884 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.20 Conformation dependent library (CDL) restraints added in 7.5 seconds 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 384 helices and 48 sheets defined 37.4% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.31 Creating SS restraints... Processing helix chain 'A' and resid 43 through 46 No H-bonds generated for 'chain 'A' and resid 43 through 46' Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.516A pdb=" N ASN A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 230 No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.007A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.778A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 408 through 430 removed outlier: 3.627A pdb=" N SER A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 449 through 453 Processing helix chain 'A' and resid 455 through 458 No H-bonds generated for 'chain 'A' and resid 455 through 458' Processing helix chain 'A' and resid 483 through 490 removed outlier: 3.623A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.994A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 568 Processing helix chain 'A' and resid 579 through 586 removed outlier: 4.190A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 661 removed outlier: 3.923A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 706 removed outlier: 3.573A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'B' and resid 43 through 46 No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 86 through 92 removed outlier: 3.518A pdb=" N ASN B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 211 through 225 removed outlier: 3.602A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 230 No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 251 through 260 removed outlier: 4.007A pdb=" N ALA B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.778A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 333 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS B 384 " --> pdb=" O ILE B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 408 through 430 removed outlier: 3.627A pdb=" N SER B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 444 No H-bonds generated for 'chain 'B' and resid 442 through 444' Processing helix chain 'B' and resid 449 through 453 Processing helix chain 'B' and resid 455 through 458 No H-bonds generated for 'chain 'B' and resid 455 through 458' Processing helix chain 'B' and resid 483 through 490 removed outlier: 3.622A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 498 Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 553 removed outlier: 3.994A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 568 Processing helix chain 'B' and resid 579 through 586 removed outlier: 4.191A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 661 removed outlier: 3.923A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 749 through 763 Processing helix chain 'C' and resid 43 through 46 No H-bonds generated for 'chain 'C' and resid 43 through 46' Processing helix chain 'C' and resid 86 through 92 removed outlier: 3.517A pdb=" N ASN C 90 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 230 No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 251 through 260 removed outlier: 4.007A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 282 through 295 removed outlier: 3.779A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 400 No H-bonds generated for 'chain 'C' and resid 398 through 400' Processing helix chain 'C' and resid 408 through 430 removed outlier: 3.626A pdb=" N SER C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 444 No H-bonds generated for 'chain 'C' and resid 442 through 444' Processing helix chain 'C' and resid 449 through 453 Processing helix chain 'C' and resid 455 through 458 No H-bonds generated for 'chain 'C' and resid 455 through 458' Processing helix chain 'C' and resid 483 through 490 removed outlier: 3.623A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 498 Processing helix chain 'C' and resid 501 through 506 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 553 removed outlier: 3.994A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 568 Processing helix chain 'C' and resid 579 through 586 removed outlier: 4.190A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 661 removed outlier: 3.924A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 706 removed outlier: 3.575A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'D' and resid 43 through 46 No H-bonds generated for 'chain 'D' and resid 43 through 46' Processing helix chain 'D' and resid 86 through 89 No H-bonds generated for 'chain 'D' and resid 86 through 89' Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 230 No H-bonds generated for 'chain 'D' and resid 227 through 230' Processing helix chain 'D' and resid 251 through 260 removed outlier: 4.008A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.779A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS D 384 " --> pdb=" O ILE D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 400 No H-bonds generated for 'chain 'D' and resid 398 through 400' Processing helix chain 'D' and resid 408 through 430 removed outlier: 3.626A pdb=" N SER D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 444 No H-bonds generated for 'chain 'D' and resid 442 through 444' Processing helix chain 'D' and resid 449 through 453 Processing helix chain 'D' and resid 455 through 458 No H-bonds generated for 'chain 'D' and resid 455 through 458' Processing helix chain 'D' and resid 483 through 490 removed outlier: 3.622A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 498 Processing helix chain 'D' and resid 501 through 506 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 553 removed outlier: 3.993A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 568 Processing helix chain 'D' and resid 579 through 586 removed outlier: 4.190A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 661 removed outlier: 3.923A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 739 Processing helix chain 'D' and resid 749 through 763 Processing helix chain 'E' and resid 43 through 46 No H-bonds generated for 'chain 'E' and resid 43 through 46' Processing helix chain 'E' and resid 86 through 89 No H-bonds generated for 'chain 'E' and resid 86 through 89' Processing helix chain 'E' and resid 135 through 139 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU E 218 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 230 No H-bonds generated for 'chain 'E' and resid 227 through 230' Processing helix chain 'E' and resid 251 through 260 removed outlier: 4.008A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 282 through 295 removed outlier: 3.777A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 291 " --> pdb=" O ARG E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE E 380 " --> pdb=" O GLY E 376 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS E 384 " --> pdb=" O ILE E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 400 No H-bonds generated for 'chain 'E' and resid 398 through 400' Processing helix chain 'E' and resid 408 through 430 removed outlier: 3.626A pdb=" N SER E 416 " --> pdb=" O ALA E 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN E 421 " --> pdb=" O GLU E 417 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 444 No H-bonds generated for 'chain 'E' and resid 442 through 444' Processing helix chain 'E' and resid 449 through 453 Processing helix chain 'E' and resid 455 through 458 No H-bonds generated for 'chain 'E' and resid 455 through 458' Processing helix chain 'E' and resid 483 through 490 removed outlier: 3.622A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 498 Processing helix chain 'E' and resid 501 through 506 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 553 removed outlier: 3.993A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 568 Processing helix chain 'E' and resid 579 through 586 removed outlier: 4.191A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 661 removed outlier: 3.924A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 739 Processing helix chain 'E' and resid 749 through 763 Processing helix chain 'F' and resid 43 through 46 No H-bonds generated for 'chain 'F' and resid 43 through 46' Processing helix chain 'F' and resid 86 through 89 No H-bonds generated for 'chain 'F' and resid 86 through 89' Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU F 218 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 230 No H-bonds generated for 'chain 'F' and resid 227 through 230' Processing helix chain 'F' and resid 251 through 260 removed outlier: 4.008A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 276 Processing helix chain 'F' and resid 282 through 295 removed outlier: 3.778A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE F 380 " --> pdb=" O GLY F 376 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS F 384 " --> pdb=" O ILE F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 400 No H-bonds generated for 'chain 'F' and resid 398 through 400' Processing helix chain 'F' and resid 408 through 430 removed outlier: 3.626A pdb=" N SER F 416 " --> pdb=" O ALA F 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN F 421 " --> pdb=" O GLU F 417 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 444 No H-bonds generated for 'chain 'F' and resid 442 through 444' Processing helix chain 'F' and resid 449 through 453 Processing helix chain 'F' and resid 455 through 458 No H-bonds generated for 'chain 'F' and resid 455 through 458' Processing helix chain 'F' and resid 483 through 490 removed outlier: 3.623A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 498 Processing helix chain 'F' and resid 501 through 506 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 553 removed outlier: 3.993A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 568 Processing helix chain 'F' and resid 579 through 586 removed outlier: 4.190A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 661 removed outlier: 3.923A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 739 Processing helix chain 'F' and resid 749 through 763 Processing helix chain 'G' and resid 43 through 46 No H-bonds generated for 'chain 'G' and resid 43 through 46' Processing helix chain 'G' and resid 86 through 92 removed outlier: 3.518A pdb=" N ASN G 90 " --> pdb=" O ARG G 86 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN G 91 " --> pdb=" O VAL G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 139 Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE G 216 " --> pdb=" O GLN G 212 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU G 218 " --> pdb=" O ALA G 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU G 222 " --> pdb=" O GLU G 218 " (cutoff:3.500A) Proline residue: G 223 - end of helix Processing helix chain 'G' and resid 227 through 230 No H-bonds generated for 'chain 'G' and resid 227 through 230' Processing helix chain 'G' and resid 251 through 260 removed outlier: 4.008A pdb=" N ALA G 255 " --> pdb=" O LYS G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 276 Processing helix chain 'G' and resid 282 through 295 removed outlier: 3.779A pdb=" N PHE G 290 " --> pdb=" O LEU G 286 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU G 291 " --> pdb=" O ARG G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'G' and resid 350 through 352 No H-bonds generated for 'chain 'G' and resid 350 through 352' Processing helix chain 'G' and resid 355 through 358 Processing helix chain 'G' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU G 379 " --> pdb=" O THR G 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE G 380 " --> pdb=" O GLY G 376 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN G 382 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE G 383 " --> pdb=" O GLU G 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS G 384 " --> pdb=" O ILE G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 400 No H-bonds generated for 'chain 'G' and resid 398 through 400' Processing helix chain 'G' and resid 408 through 430 removed outlier: 3.627A pdb=" N SER G 416 " --> pdb=" O ALA G 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN G 421 " --> pdb=" O GLU G 417 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS G 426 " --> pdb=" O ALA G 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP G 428 " --> pdb=" O ARG G 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU G 429 " --> pdb=" O LYS G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 442 through 444 No H-bonds generated for 'chain 'G' and resid 442 through 444' Processing helix chain 'G' and resid 449 through 453 Processing helix chain 'G' and resid 455 through 458 No H-bonds generated for 'chain 'G' and resid 455 through 458' Processing helix chain 'G' and resid 483 through 490 removed outlier: 3.623A pdb=" N GLU G 488 " --> pdb=" O ASP G 484 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 498 Processing helix chain 'G' and resid 501 through 506 Processing helix chain 'G' and resid 524 through 534 Processing helix chain 'G' and resid 544 through 553 removed outlier: 3.992A pdb=" N MET G 550 " --> pdb=" O GLU G 546 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP G 551 " --> pdb=" O LEU G 547 " (cutoff:3.500A) Processing helix chain 'G' and resid 558 through 568 Processing helix chain 'G' and resid 579 through 586 removed outlier: 4.189A pdb=" N ILE G 582 " --> pdb=" O LEU G 579 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 609 Processing helix chain 'G' and resid 631 through 634 Processing helix chain 'G' and resid 650 through 661 removed outlier: 3.923A pdb=" N ALA G 655 " --> pdb=" O LYS G 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 672 through 678 Processing helix chain 'G' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU G 706 " --> pdb=" O SER G 702 " (cutoff:3.500A) Processing helix chain 'G' and resid 733 through 739 Processing helix chain 'G' and resid 749 through 763 Processing helix chain 'H' and resid 43 through 46 No H-bonds generated for 'chain 'H' and resid 43 through 46' Processing helix chain 'H' and resid 86 through 89 No H-bonds generated for 'chain 'H' and resid 86 through 89' Processing helix chain 'H' and resid 135 through 139 Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'H' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN H 215 " --> pdb=" O LYS H 211 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE H 216 " --> pdb=" O GLN H 212 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS H 217 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU H 218 " --> pdb=" O ALA H 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU H 222 " --> pdb=" O GLU H 218 " (cutoff:3.500A) Proline residue: H 223 - end of helix Processing helix chain 'H' and resid 227 through 230 No H-bonds generated for 'chain 'H' and resid 227 through 230' Processing helix chain 'H' and resid 251 through 260 removed outlier: 4.008A pdb=" N ALA H 255 " --> pdb=" O LYS H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 272 through 276 Processing helix chain 'H' and resid 282 through 295 removed outlier: 3.779A pdb=" N PHE H 290 " --> pdb=" O LEU H 286 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU H 291 " --> pdb=" O ARG H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'H' and resid 350 through 352 No H-bonds generated for 'chain 'H' and resid 350 through 352' Processing helix chain 'H' and resid 355 through 358 Processing helix chain 'H' and resid 374 through 385 removed outlier: 3.595A pdb=" N GLU H 379 " --> pdb=" O THR H 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE H 380 " --> pdb=" O GLY H 376 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN H 382 " --> pdb=" O LEU H 378 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE H 383 " --> pdb=" O GLU H 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS H 384 " --> pdb=" O ILE H 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 398 through 400 No H-bonds generated for 'chain 'H' and resid 398 through 400' Processing helix chain 'H' and resid 408 through 430 removed outlier: 3.627A pdb=" N SER H 416 " --> pdb=" O ALA H 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN H 421 " --> pdb=" O GLU H 417 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS H 426 " --> pdb=" O ALA H 422 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP H 428 " --> pdb=" O ARG H 424 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU H 429 " --> pdb=" O LYS H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 442 through 444 No H-bonds generated for 'chain 'H' and resid 442 through 444' Processing helix chain 'H' and resid 449 through 453 Processing helix chain 'H' and resid 455 through 458 No H-bonds generated for 'chain 'H' and resid 455 through 458' Processing helix chain 'H' and resid 483 through 490 removed outlier: 3.623A pdb=" N GLU H 488 " --> pdb=" O ASP H 484 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 498 Processing helix chain 'H' and resid 501 through 506 Processing helix chain 'H' and resid 524 through 534 Processing helix chain 'H' and resid 544 through 553 removed outlier: 3.993A pdb=" N MET H 550 " --> pdb=" O GLU H 546 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP H 551 " --> pdb=" O LEU H 547 " (cutoff:3.500A) Processing helix chain 'H' and resid 558 through 568 Processing helix chain 'H' and resid 579 through 586 removed outlier: 4.191A pdb=" N ILE H 582 " --> pdb=" O LEU H 579 " (cutoff:3.500A) Processing helix chain 'H' and resid 599 through 609 Processing helix chain 'H' and resid 631 through 634 Processing helix chain 'H' and resid 650 through 661 removed outlier: 3.923A pdb=" N ALA H 655 " --> pdb=" O LYS H 651 " (cutoff:3.500A) Processing helix chain 'H' and resid 672 through 678 Processing helix chain 'H' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU H 706 " --> pdb=" O SER H 702 " (cutoff:3.500A) Processing helix chain 'H' and resid 733 through 739 Processing helix chain 'H' and resid 749 through 763 Processing helix chain 'I' and resid 43 through 46 No H-bonds generated for 'chain 'I' and resid 43 through 46' Processing helix chain 'I' and resid 86 through 89 No H-bonds generated for 'chain 'I' and resid 86 through 89' Processing helix chain 'I' and resid 135 through 139 Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN I 215 " --> pdb=" O LYS I 211 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE I 216 " --> pdb=" O GLN I 212 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS I 217 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU I 218 " --> pdb=" O ALA I 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU I 222 " --> pdb=" O GLU I 218 " (cutoff:3.500A) Proline residue: I 223 - end of helix Processing helix chain 'I' and resid 227 through 230 No H-bonds generated for 'chain 'I' and resid 227 through 230' Processing helix chain 'I' and resid 251 through 260 removed outlier: 4.007A pdb=" N ALA I 255 " --> pdb=" O LYS I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 276 Processing helix chain 'I' and resid 282 through 295 removed outlier: 3.779A pdb=" N PHE I 290 " --> pdb=" O LEU I 286 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU I 291 " --> pdb=" O ARG I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 333 Processing helix chain 'I' and resid 350 through 352 No H-bonds generated for 'chain 'I' and resid 350 through 352' Processing helix chain 'I' and resid 355 through 358 Processing helix chain 'I' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU I 379 " --> pdb=" O THR I 375 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE I 380 " --> pdb=" O GLY I 376 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN I 382 " --> pdb=" O LEU I 378 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE I 383 " --> pdb=" O GLU I 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS I 384 " --> pdb=" O ILE I 380 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 400 No H-bonds generated for 'chain 'I' and resid 398 through 400' Processing helix chain 'I' and resid 408 through 430 removed outlier: 3.626A pdb=" N SER I 416 " --> pdb=" O ALA I 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN I 421 " --> pdb=" O GLU I 417 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS I 426 " --> pdb=" O ALA I 422 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP I 428 " --> pdb=" O ARG I 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU I 429 " --> pdb=" O LYS I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 442 through 444 No H-bonds generated for 'chain 'I' and resid 442 through 444' Processing helix chain 'I' and resid 449 through 453 Processing helix chain 'I' and resid 455 through 458 No H-bonds generated for 'chain 'I' and resid 455 through 458' Processing helix chain 'I' and resid 483 through 490 removed outlier: 3.622A pdb=" N GLU I 488 " --> pdb=" O ASP I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 498 Processing helix chain 'I' and resid 501 through 506 Processing helix chain 'I' and resid 524 through 534 Processing helix chain 'I' and resid 544 through 553 removed outlier: 3.993A pdb=" N MET I 550 " --> pdb=" O GLU I 546 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP I 551 " --> pdb=" O LEU I 547 " (cutoff:3.500A) Processing helix chain 'I' and resid 558 through 568 Processing helix chain 'I' and resid 579 through 586 removed outlier: 4.191A pdb=" N ILE I 582 " --> pdb=" O LEU I 579 " (cutoff:3.500A) Processing helix chain 'I' and resid 599 through 609 Processing helix chain 'I' and resid 631 through 634 Processing helix chain 'I' and resid 650 through 661 removed outlier: 3.924A pdb=" N ALA I 655 " --> pdb=" O LYS I 651 " (cutoff:3.500A) Processing helix chain 'I' and resid 672 through 678 Processing helix chain 'I' and resid 684 through 706 removed outlier: 3.575A pdb=" N GLU I 706 " --> pdb=" O SER I 702 " (cutoff:3.500A) Processing helix chain 'I' and resid 733 through 739 Processing helix chain 'I' and resid 749 through 763 Processing helix chain 'J' and resid 43 through 46 No H-bonds generated for 'chain 'J' and resid 43 through 46' Processing helix chain 'J' and resid 86 through 92 removed outlier: 3.517A pdb=" N ASN J 90 " --> pdb=" O ARG J 86 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN J 91 " --> pdb=" O VAL J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 139 Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 211 through 225 removed outlier: 3.604A pdb=" N GLN J 215 " --> pdb=" O LYS J 211 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE J 216 " --> pdb=" O GLN J 212 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS J 217 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU J 218 " --> pdb=" O ALA J 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU J 222 " --> pdb=" O GLU J 218 " (cutoff:3.500A) Proline residue: J 223 - end of helix Processing helix chain 'J' and resid 227 through 230 No H-bonds generated for 'chain 'J' and resid 227 through 230' Processing helix chain 'J' and resid 251 through 260 removed outlier: 4.006A pdb=" N ALA J 255 " --> pdb=" O LYS J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 276 Processing helix chain 'J' and resid 282 through 295 removed outlier: 3.779A pdb=" N PHE J 290 " --> pdb=" O LEU J 286 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU J 291 " --> pdb=" O ARG J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 333 Processing helix chain 'J' and resid 350 through 352 No H-bonds generated for 'chain 'J' and resid 350 through 352' Processing helix chain 'J' and resid 355 through 358 Processing helix chain 'J' and resid 374 through 385 removed outlier: 3.594A pdb=" N GLU J 379 " --> pdb=" O THR J 375 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE J 380 " --> pdb=" O GLY J 376 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN J 382 " --> pdb=" O LEU J 378 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE J 383 " --> pdb=" O GLU J 379 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS J 384 " --> pdb=" O ILE J 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 398 through 400 No H-bonds generated for 'chain 'J' and resid 398 through 400' Processing helix chain 'J' and resid 408 through 430 removed outlier: 3.625A pdb=" N SER J 416 " --> pdb=" O ALA J 412 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN J 421 " --> pdb=" O GLU J 417 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS J 426 " --> pdb=" O ALA J 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP J 428 " --> pdb=" O ARG J 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU J 429 " --> pdb=" O LYS J 425 " (cutoff:3.500A) Processing helix chain 'J' and resid 442 through 444 No H-bonds generated for 'chain 'J' and resid 442 through 444' Processing helix chain 'J' and resid 449 through 453 Processing helix chain 'J' and resid 455 through 458 No H-bonds generated for 'chain 'J' and resid 455 through 458' Processing helix chain 'J' and resid 483 through 490 removed outlier: 3.623A pdb=" N GLU J 488 " --> pdb=" O ASP J 484 " (cutoff:3.500A) Processing helix chain 'J' and resid 494 through 498 Processing helix chain 'J' and resid 501 through 506 Processing helix chain 'J' and resid 524 through 534 Processing helix chain 'J' and resid 544 through 553 removed outlier: 3.993A pdb=" N MET J 550 " --> pdb=" O GLU J 546 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP J 551 " --> pdb=" O LEU J 547 " (cutoff:3.500A) Processing helix chain 'J' and resid 558 through 568 Processing helix chain 'J' and resid 579 through 586 removed outlier: 4.190A pdb=" N ILE J 582 " --> pdb=" O LEU J 579 " (cutoff:3.500A) Processing helix chain 'J' and resid 599 through 609 Processing helix chain 'J' and resid 631 through 634 Processing helix chain 'J' and resid 650 through 661 removed outlier: 3.924A pdb=" N ALA J 655 " --> pdb=" O LYS J 651 " (cutoff:3.500A) Processing helix chain 'J' and resid 672 through 678 Processing helix chain 'J' and resid 684 through 706 removed outlier: 3.573A pdb=" N GLU J 706 " --> pdb=" O SER J 702 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 739 Processing helix chain 'J' and resid 749 through 763 Processing helix chain 'K' and resid 43 through 46 No H-bonds generated for 'chain 'K' and resid 43 through 46' Processing helix chain 'K' and resid 86 through 89 No H-bonds generated for 'chain 'K' and resid 86 through 89' Processing helix chain 'K' and resid 135 through 139 Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN K 215 " --> pdb=" O LYS K 211 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE K 216 " --> pdb=" O GLN K 212 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS K 217 " --> pdb=" O LEU K 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU K 218 " --> pdb=" O ALA K 214 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU K 222 " --> pdb=" O GLU K 218 " (cutoff:3.500A) Proline residue: K 223 - end of helix Processing helix chain 'K' and resid 227 through 230 No H-bonds generated for 'chain 'K' and resid 227 through 230' Processing helix chain 'K' and resid 251 through 260 removed outlier: 4.007A pdb=" N ALA K 255 " --> pdb=" O LYS K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 276 Processing helix chain 'K' and resid 282 through 295 removed outlier: 3.778A pdb=" N PHE K 290 " --> pdb=" O LEU K 286 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU K 291 " --> pdb=" O ARG K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 333 Processing helix chain 'K' and resid 350 through 352 No H-bonds generated for 'chain 'K' and resid 350 through 352' Processing helix chain 'K' and resid 355 through 358 Processing helix chain 'K' and resid 374 through 385 removed outlier: 3.594A pdb=" N GLU K 379 " --> pdb=" O THR K 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE K 380 " --> pdb=" O GLY K 376 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN K 382 " --> pdb=" O LEU K 378 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE K 383 " --> pdb=" O GLU K 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS K 384 " --> pdb=" O ILE K 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 400 No H-bonds generated for 'chain 'K' and resid 398 through 400' Processing helix chain 'K' and resid 408 through 430 removed outlier: 3.627A pdb=" N SER K 416 " --> pdb=" O ALA K 412 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN K 421 " --> pdb=" O GLU K 417 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS K 426 " --> pdb=" O ALA K 422 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP K 428 " --> pdb=" O ARG K 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU K 429 " --> pdb=" O LYS K 425 " (cutoff:3.500A) Processing helix chain 'K' and resid 442 through 444 No H-bonds generated for 'chain 'K' and resid 442 through 444' Processing helix chain 'K' and resid 449 through 453 Processing helix chain 'K' and resid 455 through 458 No H-bonds generated for 'chain 'K' and resid 455 through 458' Processing helix chain 'K' and resid 483 through 490 removed outlier: 3.623A pdb=" N GLU K 488 " --> pdb=" O ASP K 484 " (cutoff:3.500A) Processing helix chain 'K' and resid 494 through 498 Processing helix chain 'K' and resid 501 through 506 Processing helix chain 'K' and resid 524 through 534 Processing helix chain 'K' and resid 544 through 553 removed outlier: 3.995A pdb=" N MET K 550 " --> pdb=" O GLU K 546 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP K 551 " --> pdb=" O LEU K 547 " (cutoff:3.500A) Processing helix chain 'K' and resid 558 through 568 Processing helix chain 'K' and resid 579 through 586 removed outlier: 4.190A pdb=" N ILE K 582 " --> pdb=" O LEU K 579 " (cutoff:3.500A) Processing helix chain 'K' and resid 599 through 609 Processing helix chain 'K' and resid 631 through 634 Processing helix chain 'K' and resid 650 through 661 removed outlier: 3.924A pdb=" N ALA K 655 " --> pdb=" O LYS K 651 " (cutoff:3.500A) Processing helix chain 'K' and resid 672 through 678 Processing helix chain 'K' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU K 706 " --> pdb=" O SER K 702 " (cutoff:3.500A) Processing helix chain 'K' and resid 733 through 739 Processing helix chain 'K' and resid 749 through 763 Processing helix chain 'L' and resid 43 through 46 No H-bonds generated for 'chain 'L' and resid 43 through 46' Processing helix chain 'L' and resid 86 through 89 No H-bonds generated for 'chain 'L' and resid 86 through 89' Processing helix chain 'L' and resid 135 through 139 Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN L 215 " --> pdb=" O LYS L 211 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE L 216 " --> pdb=" O GLN L 212 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS L 217 " --> pdb=" O LEU L 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU L 218 " --> pdb=" O ALA L 214 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU L 222 " --> pdb=" O GLU L 218 " (cutoff:3.500A) Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 227 through 230 No H-bonds generated for 'chain 'L' and resid 227 through 230' Processing helix chain 'L' and resid 251 through 260 removed outlier: 4.007A pdb=" N ALA L 255 " --> pdb=" O LYS L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 272 through 276 Processing helix chain 'L' and resid 282 through 295 removed outlier: 3.778A pdb=" N PHE L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU L 291 " --> pdb=" O ARG L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 333 Processing helix chain 'L' and resid 350 through 352 No H-bonds generated for 'chain 'L' and resid 350 through 352' Processing helix chain 'L' and resid 355 through 358 Processing helix chain 'L' and resid 374 through 385 removed outlier: 3.594A pdb=" N GLU L 379 " --> pdb=" O THR L 375 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE L 380 " --> pdb=" O GLY L 376 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN L 382 " --> pdb=" O LEU L 378 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE L 383 " --> pdb=" O GLU L 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS L 384 " --> pdb=" O ILE L 380 " (cutoff:3.500A) Processing helix chain 'L' and resid 398 through 400 No H-bonds generated for 'chain 'L' and resid 398 through 400' Processing helix chain 'L' and resid 408 through 430 removed outlier: 3.627A pdb=" N SER L 416 " --> pdb=" O ALA L 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN L 421 " --> pdb=" O GLU L 417 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS L 426 " --> pdb=" O ALA L 422 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP L 428 " --> pdb=" O ARG L 424 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU L 429 " --> pdb=" O LYS L 425 " (cutoff:3.500A) Processing helix chain 'L' and resid 442 through 444 No H-bonds generated for 'chain 'L' and resid 442 through 444' Processing helix chain 'L' and resid 449 through 453 Processing helix chain 'L' and resid 455 through 458 No H-bonds generated for 'chain 'L' and resid 455 through 458' Processing helix chain 'L' and resid 483 through 490 removed outlier: 3.621A pdb=" N GLU L 488 " --> pdb=" O ASP L 484 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 498 Processing helix chain 'L' and resid 501 through 506 Processing helix chain 'L' and resid 524 through 534 Processing helix chain 'L' and resid 544 through 553 removed outlier: 3.994A pdb=" N MET L 550 " --> pdb=" O GLU L 546 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP L 551 " --> pdb=" O LEU L 547 " (cutoff:3.500A) Processing helix chain 'L' and resid 558 through 568 Processing helix chain 'L' and resid 579 through 586 removed outlier: 4.190A pdb=" N ILE L 582 " --> pdb=" O LEU L 579 " (cutoff:3.500A) Processing helix chain 'L' and resid 599 through 609 Processing helix chain 'L' and resid 631 through 634 Processing helix chain 'L' and resid 650 through 661 removed outlier: 3.924A pdb=" N ALA L 655 " --> pdb=" O LYS L 651 " (cutoff:3.500A) Processing helix chain 'L' and resid 672 through 678 Processing helix chain 'L' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU L 706 " --> pdb=" O SER L 702 " (cutoff:3.500A) Processing helix chain 'L' and resid 733 through 739 Processing helix chain 'L' and resid 749 through 763 Processing sheet with id= A, first strand: chain 'A' and resid 66 through 70 removed outlier: 3.679A pdb=" N VAL A 57 " --> pdb=" O CYS A 69 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 58 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN A 103 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 163 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 154 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 156 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 159 " --> pdb=" O GLY A 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 365 through 367 removed outlier: 7.134A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 643 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 66 through 70 removed outlier: 3.679A pdb=" N VAL B 57 " --> pdb=" O CYS B 69 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 58 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN B 103 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.945A pdb=" N PHE B 152 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 163 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 154 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 156 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 159 " --> pdb=" O GLY B 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 365 through 367 removed outlier: 7.134A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 641 through 645 removed outlier: 4.047A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 643 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 66 through 70 removed outlier: 3.679A pdb=" N VAL C 57 " --> pdb=" O CYS C 69 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 58 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN C 103 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE C 152 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE C 163 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 154 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY C 156 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C 159 " --> pdb=" O GLY C 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 365 through 367 removed outlier: 7.133A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 643 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 66 through 70 removed outlier: 3.678A pdb=" N VAL D 57 " --> pdb=" O CYS D 69 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 58 " --> pdb=" O GLN D 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN D 103 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE D 152 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE D 163 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D 154 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL D 161 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY D 156 " --> pdb=" O ARG D 159 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG D 159 " --> pdb=" O GLY D 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 365 through 367 removed outlier: 7.135A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 643 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 66 through 70 removed outlier: 3.679A pdb=" N VAL E 57 " --> pdb=" O CYS E 69 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU E 58 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN E 103 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE E 152 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE E 163 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 154 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY E 156 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG E 159 " --> pdb=" O GLY E 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 365 through 367 removed outlier: 7.134A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 643 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 66 through 70 removed outlier: 3.679A pdb=" N VAL F 57 " --> pdb=" O CYS F 69 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU F 58 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE F 152 " --> pdb=" O PHE F 163 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE F 163 " --> pdb=" O PHE F 152 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL F 154 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL F 161 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY F 156 " --> pdb=" O ARG F 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG F 159 " --> pdb=" O GLY F 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 365 through 367 removed outlier: 7.133A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 643 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.678A pdb=" N VAL G 57 " --> pdb=" O CYS G 69 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU G 58 " --> pdb=" O GLN G 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN G 103 " --> pdb=" O LEU G 58 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE G 152 " --> pdb=" O PHE G 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE G 163 " --> pdb=" O PHE G 152 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL G 154 " --> pdb=" O VAL G 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL G 161 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY G 156 " --> pdb=" O ARG G 159 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG G 159 " --> pdb=" O GLY G 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'G' and resid 365 through 367 removed outlier: 7.135A pdb=" N ALA G 299 " --> pdb=" O ILE G 342 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N MET G 344 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE G 301 " --> pdb=" O MET G 344 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA G 346 " --> pdb=" O ILE G 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE G 303 " --> pdb=" O ALA G 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE G 265 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE G 302 " --> pdb=" O PHE G 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE G 267 " --> pdb=" O PHE G 302 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN G 641 " --> pdb=" O GLY G 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE G 643 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE G 619 " --> pdb=" O VAL G 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE G 516 " --> pdb=" O ILE G 619 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY G 621 " --> pdb=" O PHE G 516 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY G 518 " --> pdb=" O GLY G 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR G 623 " --> pdb=" O GLY G 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE G 620 " --> pdb=" O CYS G 572 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU G 574 " --> pdb=" O ILE G 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA G 622 " --> pdb=" O LEU G 574 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE G 576 " --> pdb=" O ALA G 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN G 538 " --> pdb=" O VAL G 573 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE G 575 " --> pdb=" O ASN G 538 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE G 540 " --> pdb=" O PHE G 575 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 66 through 70 removed outlier: 3.679A pdb=" N VAL H 57 " --> pdb=" O CYS H 69 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU H 58 " --> pdb=" O GLN H 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN H 103 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE H 152 " --> pdb=" O PHE H 163 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE H 163 " --> pdb=" O PHE H 152 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL H 154 " --> pdb=" O VAL H 161 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL H 161 " --> pdb=" O VAL H 154 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY H 156 " --> pdb=" O ARG H 159 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG H 159 " --> pdb=" O GLY H 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'H' and resid 365 through 367 removed outlier: 7.134A pdb=" N ALA H 299 " --> pdb=" O ILE H 342 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N MET H 344 " --> pdb=" O ALA H 299 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE H 301 " --> pdb=" O MET H 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA H 346 " --> pdb=" O ILE H 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE H 303 " --> pdb=" O ALA H 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE H 265 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE H 302 " --> pdb=" O PHE H 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE H 267 " --> pdb=" O PHE H 302 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN H 641 " --> pdb=" O GLY H 513 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE H 643 " --> pdb=" O LEU H 515 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE H 619 " --> pdb=" O VAL H 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE H 516 " --> pdb=" O ILE H 619 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY H 621 " --> pdb=" O PHE H 516 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY H 518 " --> pdb=" O GLY H 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR H 623 " --> pdb=" O GLY H 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE H 620 " --> pdb=" O CYS H 572 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU H 574 " --> pdb=" O ILE H 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA H 622 " --> pdb=" O LEU H 574 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE H 576 " --> pdb=" O ALA H 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN H 538 " --> pdb=" O VAL H 573 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE H 575 " --> pdb=" O ASN H 538 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE H 540 " --> pdb=" O PHE H 575 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 66 through 70 removed outlier: 3.678A pdb=" N VAL I 57 " --> pdb=" O CYS I 69 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU I 58 " --> pdb=" O GLN I 103 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN I 103 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 151 through 156 removed outlier: 3.945A pdb=" N PHE I 152 " --> pdb=" O PHE I 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE I 163 " --> pdb=" O PHE I 152 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL I 154 " --> pdb=" O VAL I 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL I 161 " --> pdb=" O VAL I 154 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY I 156 " --> pdb=" O ARG I 159 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG I 159 " --> pdb=" O GLY I 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'I' and resid 365 through 367 removed outlier: 7.135A pdb=" N ALA I 299 " --> pdb=" O ILE I 342 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N MET I 344 " --> pdb=" O ALA I 299 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE I 301 " --> pdb=" O MET I 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA I 346 " --> pdb=" O ILE I 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE I 303 " --> pdb=" O ALA I 346 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE I 265 " --> pdb=" O ILE I 300 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE I 302 " --> pdb=" O PHE I 265 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE I 267 " --> pdb=" O PHE I 302 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN I 641 " --> pdb=" O GLY I 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE I 643 " --> pdb=" O LEU I 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE I 619 " --> pdb=" O VAL I 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE I 516 " --> pdb=" O ILE I 619 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY I 621 " --> pdb=" O PHE I 516 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY I 518 " --> pdb=" O GLY I 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR I 623 " --> pdb=" O GLY I 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE I 620 " --> pdb=" O CYS I 572 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU I 574 " --> pdb=" O ILE I 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA I 622 " --> pdb=" O LEU I 574 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE I 576 " --> pdb=" O ALA I 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN I 538 " --> pdb=" O VAL I 573 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE I 575 " --> pdb=" O ASN I 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE I 540 " --> pdb=" O PHE I 575 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'J' and resid 66 through 70 removed outlier: 3.678A pdb=" N VAL J 57 " --> pdb=" O CYS J 69 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU J 58 " --> pdb=" O GLN J 103 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN J 103 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'J' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE J 152 " --> pdb=" O PHE J 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE J 163 " --> pdb=" O PHE J 152 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL J 154 " --> pdb=" O VAL J 161 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL J 161 " --> pdb=" O VAL J 154 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY J 156 " --> pdb=" O ARG J 159 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG J 159 " --> pdb=" O GLY J 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'J' and resid 365 through 367 removed outlier: 7.135A pdb=" N ALA J 299 " --> pdb=" O ILE J 342 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N MET J 344 " --> pdb=" O ALA J 299 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE J 301 " --> pdb=" O MET J 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA J 346 " --> pdb=" O ILE J 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE J 303 " --> pdb=" O ALA J 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE J 265 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N PHE J 302 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE J 267 " --> pdb=" O PHE J 302 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'J' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN J 641 " --> pdb=" O GLY J 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE J 643 " --> pdb=" O LEU J 515 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE J 619 " --> pdb=" O VAL J 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE J 516 " --> pdb=" O ILE J 619 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY J 621 " --> pdb=" O PHE J 516 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY J 518 " --> pdb=" O GLY J 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR J 623 " --> pdb=" O GLY J 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE J 620 " --> pdb=" O CYS J 572 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU J 574 " --> pdb=" O ILE J 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA J 622 " --> pdb=" O LEU J 574 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE J 576 " --> pdb=" O ALA J 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN J 538 " --> pdb=" O VAL J 573 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE J 575 " --> pdb=" O ASN J 538 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE J 540 " --> pdb=" O PHE J 575 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'K' and resid 66 through 70 removed outlier: 3.678A pdb=" N VAL K 57 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU K 58 " --> pdb=" O GLN K 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN K 103 " --> pdb=" O LEU K 58 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'K' and resid 151 through 156 removed outlier: 3.945A pdb=" N PHE K 152 " --> pdb=" O PHE K 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE K 163 " --> pdb=" O PHE K 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL K 154 " --> pdb=" O VAL K 161 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL K 161 " --> pdb=" O VAL K 154 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY K 156 " --> pdb=" O ARG K 159 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG K 159 " --> pdb=" O GLY K 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'K' and resid 365 through 367 removed outlier: 7.134A pdb=" N ALA K 299 " --> pdb=" O ILE K 342 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N MET K 344 " --> pdb=" O ALA K 299 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE K 301 " --> pdb=" O MET K 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA K 346 " --> pdb=" O ILE K 301 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE K 303 " --> pdb=" O ALA K 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE K 265 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE K 302 " --> pdb=" O PHE K 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE K 267 " --> pdb=" O PHE K 302 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'K' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN K 641 " --> pdb=" O GLY K 513 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE K 643 " --> pdb=" O LEU K 515 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE K 619 " --> pdb=" O VAL K 514 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE K 516 " --> pdb=" O ILE K 619 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY K 621 " --> pdb=" O PHE K 516 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLY K 518 " --> pdb=" O GLY K 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR K 623 " --> pdb=" O GLY K 518 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ILE K 620 " --> pdb=" O CYS K 572 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU K 574 " --> pdb=" O ILE K 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA K 622 " --> pdb=" O LEU K 574 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE K 576 " --> pdb=" O ALA K 622 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN K 538 " --> pdb=" O VAL K 573 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE K 575 " --> pdb=" O ASN K 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE K 540 " --> pdb=" O PHE K 575 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'L' and resid 66 through 70 removed outlier: 3.679A pdb=" N VAL L 57 " --> pdb=" O CYS L 69 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU L 58 " --> pdb=" O GLN L 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN L 103 " --> pdb=" O LEU L 58 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'L' and resid 151 through 156 removed outlier: 3.945A pdb=" N PHE L 152 " --> pdb=" O PHE L 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE L 163 " --> pdb=" O PHE L 152 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL L 154 " --> pdb=" O VAL L 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL L 161 " --> pdb=" O VAL L 154 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY L 156 " --> pdb=" O ARG L 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG L 159 " --> pdb=" O GLY L 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'L' and resid 365 through 367 removed outlier: 7.135A pdb=" N ALA L 299 " --> pdb=" O ILE L 342 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N MET L 344 " --> pdb=" O ALA L 299 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE L 301 " --> pdb=" O MET L 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA L 346 " --> pdb=" O ILE L 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE L 303 " --> pdb=" O ALA L 346 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N PHE L 265 " --> pdb=" O ILE L 300 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE L 302 " --> pdb=" O PHE L 265 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE L 267 " --> pdb=" O PHE L 302 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'L' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN L 641 " --> pdb=" O GLY L 513 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE L 643 " --> pdb=" O LEU L 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE L 619 " --> pdb=" O VAL L 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE L 516 " --> pdb=" O ILE L 619 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY L 621 " --> pdb=" O PHE L 516 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY L 518 " --> pdb=" O GLY L 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR L 623 " --> pdb=" O GLY L 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE L 620 " --> pdb=" O CYS L 572 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU L 574 " --> pdb=" O ILE L 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA L 622 " --> pdb=" O LEU L 574 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE L 576 " --> pdb=" O ALA L 622 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN L 538 " --> pdb=" O VAL L 573 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE L 575 " --> pdb=" O ASN L 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE L 540 " --> pdb=" O PHE L 575 " (cutoff:3.500A) 1649 hydrogen bonds defined for protein. 4695 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.35 Time building geometry restraints manager: 24.49 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: 12204 1.31 - 1.44: 16656 1.44 - 1.56: 41477 1.56 - 1.69: 79 1.69 - 1.82: 576 Bond restraints: 70992 Sorted by residual: bond pdb=" C02 JDP J 901 " pdb=" N31 JDP J 901 " ideal model delta sigma weight residual 1.344 1.451 -0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" C02 JDP A 901 " pdb=" N31 JDP A 901 " ideal model delta sigma weight residual 1.344 1.451 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C02 JDP F 901 " pdb=" N31 JDP F 901 " ideal model delta sigma weight residual 1.344 1.451 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C02 JDP D 901 " pdb=" N31 JDP D 901 " ideal model delta sigma weight residual 1.344 1.451 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C02 JDP I 901 " pdb=" N31 JDP I 901 " ideal model delta sigma weight residual 1.344 1.451 -0.107 2.00e-02 2.50e+03 2.86e+01 ... (remaining 70987 not shown) Histogram of bond angle deviations from ideal: 99.36 - 109.72: 8120 109.72 - 120.08: 58444 120.08 - 130.45: 29172 130.45 - 140.81: 204 140.81 - 151.17: 12 Bond angle restraints: 95952 Sorted by residual: angle pdb=" C11 JDP A 901 " pdb=" C10 JDP A 901 " pdb=" N12 JDP A 901 " ideal model delta sigma weight residual 124.18 151.17 -26.99 3.00e+00 1.11e-01 8.10e+01 angle pdb=" C11 JDP I 901 " pdb=" C10 JDP I 901 " pdb=" N12 JDP I 901 " ideal model delta sigma weight residual 124.18 151.17 -26.99 3.00e+00 1.11e-01 8.09e+01 angle pdb=" C11 JDP K 901 " pdb=" C10 JDP K 901 " pdb=" N12 JDP K 901 " ideal model delta sigma weight residual 124.18 151.13 -26.95 3.00e+00 1.11e-01 8.07e+01 angle pdb=" C11 JDP J 901 " pdb=" C10 JDP J 901 " pdb=" N12 JDP J 901 " ideal model delta sigma weight residual 124.18 151.12 -26.94 3.00e+00 1.11e-01 8.06e+01 angle pdb=" C11 JDP H 901 " pdb=" C10 JDP H 901 " pdb=" N12 JDP H 901 " ideal model delta sigma weight residual 124.18 151.11 -26.93 3.00e+00 1.11e-01 8.06e+01 ... (remaining 95947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.18: 40958 27.18 - 54.36: 2630 54.36 - 81.54: 170 81.54 - 108.72: 12 108.72 - 135.89: 30 Dihedral angle restraints: 43800 sinusoidal: 18432 harmonic: 25368 Sorted by residual: dihedral pdb=" CA GLN K 760 " pdb=" C GLN K 760 " pdb=" N THR K 761 " pdb=" CA THR K 761 " ideal model delta harmonic sigma weight residual 180.00 147.20 32.80 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CA GLN J 760 " pdb=" C GLN J 760 " pdb=" N THR J 761 " pdb=" CA THR J 761 " ideal model delta harmonic sigma weight residual 180.00 147.25 32.75 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA GLN C 760 " pdb=" C GLN C 760 " pdb=" N THR C 761 " pdb=" CA THR C 761 " ideal model delta harmonic sigma weight residual 180.00 147.25 32.75 0 5.00e+00 4.00e-02 4.29e+01 ... (remaining 43797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 8686 0.058 - 0.117: 1832 0.117 - 0.175: 150 0.175 - 0.234: 12 0.234 - 0.292: 24 Chirality restraints: 10704 Sorted by residual: chirality pdb=" CA GLN A 760 " pdb=" N GLN A 760 " pdb=" C GLN A 760 " pdb=" CB GLN A 760 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA GLN G 760 " pdb=" N GLN G 760 " pdb=" C GLN G 760 " pdb=" CB GLN G 760 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA GLN I 760 " pdb=" N GLN I 760 " pdb=" C GLN I 760 " pdb=" CB GLN I 760 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 10701 not shown) Planarity restraints: 12636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 349 " 0.295 9.50e-02 1.11e+02 1.32e-01 1.11e+01 pdb=" NE ARG H 349 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG H 349 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG H 349 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 349 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 349 " 0.295 9.50e-02 1.11e+02 1.32e-01 1.11e+01 pdb=" NE ARG D 349 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 349 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D 349 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 349 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 349 " 0.294 9.50e-02 1.11e+02 1.32e-01 1.10e+01 pdb=" NE ARG I 349 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG I 349 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG I 349 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG I 349 " 0.014 2.00e-02 2.50e+03 ... (remaining 12633 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.17: 85 2.17 - 2.85: 24284 2.85 - 3.53: 100252 3.53 - 4.22: 166203 4.22 - 4.90: 274875 Nonbonded interactions: 565699 Sorted by model distance: nonbonded pdb=" NE2 GLN B 760 " pdb=" NE2 GLN J 760 " model vdw 1.481 3.200 nonbonded pdb=" NE2 GLN A 760 " pdb=" NE2 GLN K 760 " model vdw 1.609 3.200 nonbonded pdb=" NE2 GLN E 760 " pdb=" NE2 GLN G 760 " model vdw 1.724 3.200 nonbonded pdb=" NE2 GLN D 760 " pdb=" NE2 GLN H 760 " model vdw 1.745 3.200 nonbonded pdb=" NE2 GLN C 760 " pdb=" NE2 GLN I 760 " model vdw 1.757 3.200 ... (remaining 565694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 360 5.16 5 C 43884 2.51 5 N 12300 2.21 5 O 13200 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.350 Construct map_model_manager: 0.090 Extract box with map and model: 17.810 Check model and map are aligned: 0.770 Process input model: 134.960 Find NCS groups from input model: 3.770 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Set scattering table: 0.470 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 : 0.005 0.107 70992 Z= 0.305 Angle : 0.952 26.994 95952 Z= 0.474 Chirality : 0.048 0.292 10704 Planarity : 0.006 0.132 12636 Dihedral : 16.393 135.895 27360 Min Nonbonded Distance : 1.481 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.32 % Favored : 94.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.09), residues: 8772 helix: -0.62 (0.09), residues: 3168 sheet: 0.11 (0.21), residues: 720 loop : -1.53 (0.09), residues: 4884 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 6.167 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.6423 time to fit residues: 486.9488 Evaluate side-chains 389 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 6.022 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.5566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 739 optimal weight: 6.9990 chunk 663 optimal weight: 3.9990 chunk 368 optimal weight: 30.0000 chunk 226 optimal weight: 20.0000 chunk 447 optimal weight: 30.0000 chunk 354 optimal weight: 2.9990 chunk 686 optimal weight: 10.0000 chunk 265 optimal weight: 7.9990 chunk 417 optimal weight: 4.9990 chunk 511 optimal weight: 20.0000 chunk 795 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 215 GLN A 285 ASN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN A 602 ASN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 215 GLN B 285 ASN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN B 602 ASN ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 GLN C 215 GLN C 285 ASN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN D 215 GLN D 285 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** D 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN F 285 ASN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 ASN F 602 ASN ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 401 ASN G 602 ASN ** G 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 764 GLN H 215 GLN H 285 ASN H 327 GLN ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 401 ASN ** H 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN I 215 GLN I 285 ASN I 327 GLN ** I 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN ** I 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN J 215 GLN ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 401 ASN J 602 ASN ** J 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 215 GLN K 285 ASN ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 ASN K 602 ASN ** K 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 215 GLN L 285 ASN ** L 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 401 ASN ** L 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.066 70992 Z= 0.513 Angle : 0.783 10.258 95952 Z= 0.387 Chirality : 0.052 0.286 10704 Planarity : 0.006 0.062 12636 Dihedral : 9.251 140.978 9792 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.35 % Favored : 94.36 % Rotamer Outliers : 5.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.09), residues: 8772 helix: -0.98 (0.08), residues: 3564 sheet: -0.19 (0.17), residues: 936 loop : -1.45 (0.09), residues: 4272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 401 poor density : 429 time to evaluate : 6.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 401 outliers final: 131 residues processed: 811 average time/residue: 0.6748 time to fit residues: 938.9361 Evaluate side-chains 485 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 354 time to evaluate : 7.357 Switching outliers to nearest non-outliers outliers start: 131 outliers final: 0 residues processed: 131 average time/residue: 0.6225 time to fit residues: 155.0819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 442 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 662 optimal weight: 30.0000 chunk 541 optimal weight: 2.9990 chunk 219 optimal weight: 30.0000 chunk 796 optimal weight: 0.9980 chunk 860 optimal weight: 1.9990 chunk 709 optimal weight: 0.5980 chunk 790 optimal weight: 1.9990 chunk 271 optimal weight: 0.7980 chunk 639 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN C 285 ASN C 337 GLN ** C 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN F 337 GLN G 285 ASN ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 602 ASN ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 337 GLN I 760 GLN J 285 ASN ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 602 ASN K 285 ASN ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 602 ASN ** K 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN L 337 GLN L 533 ASN L 624 ASN L 760 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 70992 Z= 0.203 Angle : 0.619 9.286 95952 Z= 0.290 Chirality : 0.046 0.278 10704 Planarity : 0.004 0.072 12636 Dihedral : 9.168 134.531 9792 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.50 % Favored : 95.22 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.09), residues: 8772 helix: -0.60 (0.09), residues: 3540 sheet: -0.08 (0.18), residues: 936 loop : -1.24 (0.09), residues: 4296 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 411 time to evaluate : 6.105 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 outliers start: 191 outliers final: 63 residues processed: 576 average time/residue: 0.6518 time to fit residues: 653.5191 Evaluate side-chains 412 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 349 time to evaluate : 6.105 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.5502 time to fit residues: 73.2121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 787 optimal weight: 20.0000 chunk 599 optimal weight: 20.0000 chunk 413 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 380 optimal weight: 8.9990 chunk 535 optimal weight: 9.9990 chunk 799 optimal weight: 0.3980 chunk 846 optimal weight: 0.0050 chunk 417 optimal weight: 0.6980 chunk 758 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 overall best weight: 2.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN F 215 GLN ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 760 GLN ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 760 GLN ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 760 GLN ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 70992 Z= 0.271 Angle : 0.613 11.857 95952 Z= 0.292 Chirality : 0.046 0.247 10704 Planarity : 0.004 0.067 12636 Dihedral : 9.087 135.331 9792 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.50 % Favored : 95.22 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.09), residues: 8772 helix: -0.41 (0.09), residues: 3564 sheet: -0.03 (0.18), residues: 924 loop : -1.11 (0.09), residues: 4284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 374 time to evaluate : 7.391 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: 157 outliers final: 61 residues processed: 516 average time/residue: 0.6828 time to fit residues: 608.8251 Evaluate side-chains 393 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 332 time to evaluate : 6.036 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.5273 time to fit residues: 68.8204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 705 optimal weight: 0.4980 chunk 480 optimal weight: 30.0000 chunk 12 optimal weight: 6.9990 chunk 630 optimal weight: 0.9990 chunk 349 optimal weight: 20.0000 chunk 722 optimal weight: 2.9990 chunk 585 optimal weight: 20.0000 chunk 1 optimal weight: 0.0980 chunk 432 optimal weight: 1.9990 chunk 760 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS C 602 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 215 GLN G 285 ASN ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 760 GLN ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 602 ASN H 760 GLN I 602 ASN ** I 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 760 GLN ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 602 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 70992 Z= 0.209 Angle : 0.604 13.291 95952 Z= 0.283 Chirality : 0.045 0.287 10704 Planarity : 0.004 0.065 12636 Dihedral : 9.001 134.789 9792 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.27 % Favored : 95.45 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.09), residues: 8772 helix: -0.31 (0.09), residues: 3552 sheet: -0.07 (0.18), residues: 924 loop : -1.02 (0.09), residues: 4296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 361 time to evaluate : 6.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 41 residues processed: 461 average time/residue: 0.6782 time to fit residues: 539.2133 Evaluate side-chains 375 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 334 time to evaluate : 6.068 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.5824 time to fit residues: 53.8436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 284 optimal weight: 4.9990 chunk 762 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 497 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 847 optimal weight: 5.9990 chunk 703 optimal weight: 0.9990 chunk 392 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 444 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 GLN G 285 ASN ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 215 GLN ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 70992 Z= 0.405 Angle : 0.695 12.257 95952 Z= 0.339 Chirality : 0.048 0.254 10704 Planarity : 0.005 0.066 12636 Dihedral : 9.363 153.188 9792 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.87 % Favored : 94.86 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.09), residues: 8772 helix: -0.44 (0.09), residues: 3648 sheet: -0.29 (0.17), residues: 924 loop : -1.00 (0.10), residues: 4200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 336 time to evaluate : 6.113 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 outliers start: 151 outliers final: 75 residues processed: 475 average time/residue: 0.7123 time to fit residues: 573.6367 Evaluate side-chains 398 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 323 time to evaluate : 6.091 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 0 residues processed: 75 average time/residue: 0.6053 time to fit residues: 89.4501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 817 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 482 optimal weight: 0.8980 chunk 618 optimal weight: 1.9990 chunk 479 optimal weight: 10.0000 chunk 713 optimal weight: 0.9990 chunk 473 optimal weight: 6.9990 chunk 844 optimal weight: 20.0000 chunk 528 optimal weight: 0.0980 chunk 514 optimal weight: 40.0000 chunk 389 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 70992 Z= 0.207 Angle : 0.614 11.239 95952 Z= 0.289 Chirality : 0.045 0.295 10704 Planarity : 0.004 0.082 12636 Dihedral : 9.194 151.234 9792 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.96 % Favored : 95.77 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.09), residues: 8772 helix: -0.33 (0.09), residues: 3636 sheet: -0.38 (0.17), residues: 924 loop : -0.93 (0.10), residues: 4212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 350 time to evaluate : 6.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 25 residues processed: 400 average time/residue: 0.7248 time to fit residues: 503.6211 Evaluate side-chains 355 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 330 time to evaluate : 6.174 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.6179 time to fit residues: 36.8316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 522 optimal weight: 7.9990 chunk 337 optimal weight: 0.9980 chunk 504 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 163 optimal weight: 0.0170 chunk 536 optimal weight: 0.6980 chunk 575 optimal weight: 6.9990 chunk 417 optimal weight: 4.9990 chunk 78 optimal weight: 30.0000 chunk 663 optimal weight: 9.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 458 GLN ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 458 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 70992 Z= 0.198 Angle : 0.599 10.481 95952 Z= 0.280 Chirality : 0.045 0.284 10704 Planarity : 0.004 0.077 12636 Dihedral : 9.007 148.936 9792 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.13 % Favored : 95.60 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.90 (0.09), residues: 8772 helix: -0.26 (0.09), residues: 3624 sheet: -0.32 (0.17), residues: 924 loop : -0.86 (0.10), residues: 4224 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 349 time to evaluate : 6.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 10 residues processed: 382 average time/residue: 0.7399 time to fit residues: 482.7777 Evaluate side-chains 331 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 321 time to evaluate : 6.028 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5375 time to fit residues: 18.5547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 768 optimal weight: 9.9990 chunk 808 optimal weight: 30.0000 chunk 737 optimal weight: 4.9990 chunk 786 optimal weight: 2.9990 chunk 473 optimal weight: 0.0000 chunk 342 optimal weight: 2.9990 chunk 617 optimal weight: 0.9990 chunk 241 optimal weight: 0.0670 chunk 710 optimal weight: 0.8980 chunk 744 optimal weight: 10.0000 chunk 784 optimal weight: 2.9990 overall best weight: 0.9926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 70992 Z= 0.186 Angle : 0.590 11.048 95952 Z= 0.276 Chirality : 0.045 0.311 10704 Planarity : 0.004 0.073 12636 Dihedral : 8.927 146.261 9792 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.04 % Favored : 95.69 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.83 (0.09), residues: 8772 helix: -0.21 (0.09), residues: 3624 sheet: -0.26 (0.17), residues: 924 loop : -0.81 (0.10), residues: 4224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 336 time to evaluate : 6.346 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 359 average time/residue: 0.7258 time to fit residues: 449.2775 Evaluate side-chains 334 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 324 time to evaluate : 6.162 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5469 time to fit residues: 19.5765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 516 optimal weight: 0.4980 chunk 831 optimal weight: 0.5980 chunk 507 optimal weight: 5.9990 chunk 394 optimal weight: 7.9990 chunk 578 optimal weight: 2.9990 chunk 872 optimal weight: 4.9990 chunk 803 optimal weight: 4.9990 chunk 694 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 536 optimal weight: 0.5980 chunk 426 optimal weight: 0.3980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN F 458 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 70992 Z= 0.188 Angle : 0.601 11.427 95952 Z= 0.281 Chirality : 0.045 0.319 10704 Planarity : 0.004 0.069 12636 Dihedral : 8.843 143.769 9792 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.34 % Favored : 95.38 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.77 (0.09), residues: 8772 helix: -0.18 (0.09), residues: 3624 sheet: -0.21 (0.17), residues: 924 loop : -0.77 (0.10), residues: 4224 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 329 time to evaluate : 6.186 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 338 average time/residue: 0.7206 time to fit residues: 421.0569 Evaluate side-chains 334 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 328 time to evaluate : 6.132 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5640 time to fit residues: 16.1606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 552 optimal weight: 30.0000 chunk 740 optimal weight: 9.9990 chunk 212 optimal weight: 0.9990 chunk 640 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 696 optimal weight: 5.9990 chunk 291 optimal weight: 0.9980 chunk 714 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.116126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.072408 restraints weight = 165084.609| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.90 r_work: 0.2846 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 70992 Z= 0.288 Angle : 0.634 11.039 95952 Z= 0.303 Chirality : 0.046 0.335 10704 Planarity : 0.005 0.075 12636 Dihedral : 9.050 150.659 9792 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.66 % Favored : 95.09 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.78 (0.09), residues: 8772 helix: -0.21 (0.09), residues: 3636 sheet: -0.32 (0.17), residues: 924 loop : -0.72 (0.10), residues: 4212 =============================================================================== Job complete usr+sys time: 11972.05 seconds wall clock time: 214 minutes 17.80 seconds (12857.80 seconds total)